Track Database Definition

The remainder of this document is divided into the following sections and should be used as a ready reference.

Common trackDb settings
Settings by track type – with examples
- bed/bigBed: Item or region tracks
- wig/bigWig/bedGraph: Signal graphing tracks
- genePred: Gene models and predictions
- bam: Compressed Sequence Alignment/Map tracks
- pgSnp: Personal Genome SNP tracks
- vcfTabix: Variant Call Format
- psl: Sequence alignments
- chain and netAlign: Paired sequence alignments
- wigMaf: Multiple alignments
- expRatio: Microarray expression data
- snp: Short genetic variants from dbSNP
- Specialize or rarely used:
  altGraphX, bedDetail, clonePos, ctgPos, downloadsOnly, encodeFiveC, factorSource, rmsk and snake.
Grouping tracks into sets and hierarchies – with examples
Special settings for custom tracks
Obscure or special cases – (aka Rejections)
Table of Contents

Open/close all details.

Common trackDb settings

Common Settings

`track`
`type`
`shortLabel`
`longLabel`
`visibility`
`html`

Common Optional Settings

`bigDataUrl <url/relativePath>`
`boxedCfg <on/off>`
`color <red,green,blue>`
`altColor <red,green,blue>`
`chromosomes <chr1,chr2,...>`
`configureByPopup <on/off>`
`dataVersion <str>`
Related settings: `directUrl <url>`
`hgsid on`
`iframeUrl <url>`
`iframeOptions <string>`
`otherDb <otherDb>`
`origAssembly <db>`
`pennantIcon <icon> [html [tip]]`
`priority <float>`
`release <alpha/beta/public>[,beta/public]`
`table <tableName>`
`tableBrowser <off/on> [table1 ...]`
`url <url>` `urlLabel <label>` `idInUrlSql <sql for id>`
`wgEncode on`

Settings by track type

Many settings are valid only for certain types of tracks. These track types are described below along with the settings specific to their types.

bed/bigBed - Item or region track settings

`type bed <3-12> [+/.]` `type bigBed <3-12> [+/.]`
`type bed5FloatScore` `type bedRnaElements` `type broadPeak` `type coloredExon` `type gvf` `type ld2` `type narrowPeak` `type peptideMapping`
`bigDataUrl <url/relativePath>`
`colorByStrand <red,green,blue> <red,green,blue>`
`compareGenomeLinks <db[.table[.column]]=label> [db[.table[.column] =label …]`
`denseCoverage <maxVal>`
`exonArrows <on/off>`
`<column>Filter <low>[:<high>]` `scoreFilter <low>[:<high>]` `pValueFilter` `qValueFilter` `signalFilter` `<column>FilterLimits <low>[:<high>]` `<column>FilterByRange <off/on>`
`filterBy <field1:title=[+]opt1a...> [field2:title=[+]opt2a...]`
`itemRgb on`
`maxItems <integer>`
`maxWindowToDraw <integer>`
`minGrayLevel <1-9>`
`noScoreFilter on`
`spectrum on` `scoreMax <integer>` `scoreMin <integer>`
`thickDrawItem <off/on>`

Less frequently used item track settings
`bedFilter on`
`bedNameLabel <label>`
Related settings: `baseColorUseSequence < <extFile {seqTable} <extFile> / hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss >`
`baseColorUseCds <given/table <table>>`
`baseColorDefault <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>`
`baseColorTickColor <lighterShade/contrastingColor>`
`showDiffBasesAllScales on`
`showDiffBasesMaxZoom <basesPerPixel>`
`showCdsAllScales`
`showCdsMaxZoom <basesPerPixel>`
`exonArrowsDense <off/on>`
`itemDetailsHtmlTable <table>`
`itemImagePath <path> <suffix>` `itemBigImagePath <path> <suffix>`
`mafTrack <trackName>`
`nextExonText <str>` `prevExonText <str>`
`showTopScorers #`
Examples of item base types

wig,bigWig - Signal graphing track settings

`type wig <low#> <high#>` `type bigWig <#> <#>`
`type bedGraph <field>` `minLimit <#>` `maxLimit<#>`
`alwaysZero <off/on>`
`autoScale <off/on>`
`bigDataUrl <url/relativePath>`
`graphTypeDefault points`
`maxHeightPixels <max:default:min>`
`maxWindowToQuery <integer>`
`spanList <s1>[,s2…]`
`smoothingWindow <off/1-16>`
`transformFunc <NONE/LOG>`
`viewLimits <lower:upper>` `viewLimitsMax <lower:upper>`
`wigColorBy <bedTable>`
`windowingFunction <mean/mean+whiskers/maximum/minimum>`
`yLineMark <#>` `yLineOnOff <off/on>` `gridDefault on`
Examples of signal graphing tracks

genePred - Gene model track settings

`type genePred [pepTable [mrnaTable]]`
Related settings: `geneClasses <cl1 cl2...>`
`gClass_<xxx> <red,green,blue>`
`itemClassTbl <table>`
`itemClassNameColumn <col>`
`itemClassClassColumn <col>`
`filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]`
`autoTranslate 0`
`intronGap <#bases>`
`defaultLinkedTables <table1>[,table2...]`
`idXref <idColumn> <altIdColumn>`
`oldToNew <tableName>`
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. baseColorUseSequence, baseColorDefault, itemDetailsHtmlTable, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom
Examples of genePred tracks

bam - Compressed Sequence Alignment track settings

`type bam`
`bigDataUrl <url/relativePath>`
Related settings: `bamColorMode <strand/gray/tag/off>`
`bamGrayMode <aliQual/baseQual/unpaired>` `aliQualRange <min:max>` `baseQualRange <min:max>`
`bamColorTag <XX>`
`noColorTag .`
`bamSkipPrintQualScore .`
`indelDoubleInsert <off/on>` `indelQueryInsert <off/on>` `indelPolyA <off/on>`
`minAliQual <#>`
Related settings: `pairEndsByName .`
`pairSearchRange <#>`
`showNames <on/off>`
Additional settings found in the "Item or region tracks" section are also available for displaying bam tags. baseColorUseSequence, baseColorDefault, maxWindowToDraw, showDiffBasesAllScales, showDiffBasesMaxZoom
Example for bam track:

pgSnp - Personal Genome SNP track settings

`type pgSnp`
`pgPolyphenPredTab <arg>`
`pgSiftPredTab <arg>`
Example of a Personal Genome SNP track:

vcfTabix - Variant Call Format (indexed by tabix) track settings

`type vcfTabix`
`bigDataUrl <url/relativePath>`
Additional settings found in the "Item or region tracks" section are also available for displaying Variant Call Format tracks. maxWindowToDraw
Example of a VCF track:

psl - Sequence alignment tracks settings

`type psl <subtype> [otherDb]`
`blastRef <assembly.table>`
`colorChromDefault off`
`pred <assembly.table>`
`pslSequence <no/all/different>`
`transMapGene <assembly.table>` `transMapInfo <table>` `transMapSrc <assembly.table>` `transMapTypeDesc <label>`
`ucscRetroInfo`
Additional settings defined elsewhere in this document are also available for displaying psl tracks. baseColorUseSequence, baseColorDefault, chainLinearGap, chainMinScore, indelDoubleInsert, indelQueryInsert, indelPolyA, itemDetailsHtmlTable, matrix, matrixHeader, maxItems, maxWindowToDraw, showCdsAllScales, showCdsMaxZoom, showDiffBasesAllScales, showDiffBasesMaxZoom, spectrum
Examples of psl alignment tracks

chain and netAlign - paired species alignment track settings

`type chain <otherDb>` `otherDb <otherDb>`
`type netAlign <otherDb> <otherChainTable>` `otherDb <otherDb>`
`chainColor <scheme>`
`chainLinearGap <loose/medium>`
`chainMinScore <#>`
`chainNormScoreAvailable <yes/no>`
`matrix <size> <#,#,#,#,…>` `matrixHeader <b1,b2,b3,b4>` `$matrix` token in html.
`spectrum on`
Examples of chain and netAlign tracks

wigMaf - Multiple alignment track settings

`type wigMaf <minVal> <maxVal>`
`frames <table>`
`irows off`
`itemFirstCharCase noChange`
`pairwiseHeight <#>`
`speciesCodonDefault <species>`
`speciesDefaultOff <species1> [species2 ...]`
Related settings: `speciesOrder <species1> [species2 …]`
`speciesGroups <sgroup1> [sgroup2 …]` `sGroup_<sgroupN> <species1> [species2 …]`
`summary <tableName>`
`treeImage <imageFile>`
`wiggle <table1> <leftLabel1> <uiLabel1> [table2 leftLabel2 uiLabelN ...]`
Examples of wigMaf tracks

expRatio - Microarray expression track settings

`type expRatio`
`expDrawExons on`
`expScale <#>`
`expStep <#>`
`expTable <tableName>`
`groupings <fileName>`
Example of an expRatio track:

snp - Short genetic variants from dbSNP track settings

`type bed 6 +`
`chimpDb <db>`
`chimpMacaqueOrthoTable <table>`
`chimpOrangMacOrthoTable <table>`
`codingAnnoLabel_<table> <text>`
`codingAnnotations <table>[,table]`
`defaultGeneTracks <genesTrack>[,genesTrack]`
`defaultMaxWeight <1\|2\|3>`
`hapmapPhase <II\|III>`
`macaqueDb <db>`
`orangDb <db>`
`snpExceptions <table>`
`snpExceptionDesc <table>`
`snpSeq <table>`
`snpSeqFile <path>`
Additional settings found in the "Item or region tracks" section are also available for displaying snp tracks. maxWindowToDraw
Example of a snp track:

Specialized or rarely used types:

NONE OF THESE ARE FOR HUBS. Nor are any of their settings.

altGraphX - Alternate splicing gene model track settings

`type altGraphX`
Example of an altGraphX track:

bedDetail - Text extended bed track settings

`type bedDetail <#>`
Additional settings defined elsewhere in this document are also available for displaying bedDetail tracks. itemRgb, url, urlLabel TODO: Currently almost no settings or configuration options are supported by bedDetail tracks. However, there is very little, in principle, that should prevent adding support for almost all the "Item or region tracks" settings.
Example of a bedDetail track:

clonePos - Genome coverage track settings

`type clonePos`
Example of a clonePos track:

ctgPos - Physical map contigs track settings

`type ctgPos`
Example of a ctgPos track:

downloadsOnly - Specialized downloadable file track settings

`type downloadsOnly`
`fileSortOrder ...`
Example of a Downloads Only track:

encodeFiveC - Five C Chromatin interaction track settings

`type encodeFiveC`
`interTable <tableName>`
`interTableKind <label>`
Example of an encodeFiveC track:

factorSource - Combined items track settings

`type factorSource`
`sourceTable <table>`
`inputTrackTable <table>`
`inputTableFieldDisplay <f1> [f2...]`
`filterBy <field1:title=[+]option1a...> [field2:title=[+]opt2a...]`
`motifTable <on>`
`motifTable <table>`
`motifPwmTable <table>`
`motifMapTable <table>`
`motifMaxWindow <window size>`
Example of a factorSource track:

rmsk - Repeat masking track settings

`type rmsk`
Additional settings found in the "Item or region tracks" section are also available for displaying gene models. maxWindowToDraw, spectrum
Example of a Repeat Masking track:

snake - Self referencing alignment track settings

`type snake <db>` `otherDb <otherDb>`
Additional settings found in the "Item or region tracks" section are also available for displaying snake tracks. maxWindowToDraw, spectrum
Example of a snake track:

Grouping tracks into sets and hierarchies

All tracks have to be assigned to one predefined track group ("Mapping and sequencing", "Genes", etc).
In addition and depending on how closely related they are, tracks can be organized into one of three hierarchical containers:

"multiWig" container: when the tracks are all in signal (wiggle or bigWig) format and it makes sense to overlay them.
Example: a set of bigWig tracks with H3K27ac signal, all on the same scale
"composite" container: when the tracks are expected to be configured together or have an internal subgrouping, like cell type or cell treatment.
Example: a set of ChIP-bigBeds in three different cell types
"superTrack" container: when the tracks share no specific configuration and you mostly want to show them together.
Example: a set of composite tracks or a mix of bigBed, bigWig and bam

Predefined major track groupings setting

`group <groupId>`
Example of a track belonging to a predefined group:

Supertrack (Folders) track settings

`superTrack on`
`parent <superTrack>`
Example of a Supertrack:

Composite track settings

`compositeTrack on`
`parent <composite> [off/on]`
`allButtonPair on`
`centerLabelsDense <off/on>`
`dragAndDrop on`
Example of a Composite track:

Composite track subgroup settings

`subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a> [mTag1b=mTitle1b…]` `subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a> [mTag2b= mTitle2b…]`
`subGroups <gTag1=mTag1?> [gTag2= mTag2?]`
`dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]`
`filterComposite <dim[A/B/C][=one]> [dimB dimC ...]`
`dimension<?>checked <mTag1a> [mTag1b …]`
`controlledVocabulary <pathToFile> <gTag#=mdbVar> [gTag#=mdbVar …]`
`sortOrder <gTag#=+/-> [gTag#=- …]`
`fileSortOrder <var=val> [var=val ...]`
Examples of Composite tracks with Subgroups

Composite track View settings

`subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b…]` `track <viewName>` `view <viewTag>`
`subGroups view=<vTag1>…` `parent <viewName> [off/on]`
`viewUi on`
`configurable <off/on>`
Example of a Composite track with Views:

Aggregate or Overlay track settings

`container multiWig`
`parent <containerTrack>`
`aggregate <transparentOverlay/stacked/solidOverlay/none>`
`showSubtrackColorOnUi on`
Example of an Aggregate track:

Special settings for custom tracks

Custom track specific settings

`genome`
`offset`
The following trackDb style settings are only set internally by the hgCustom CGI code.
`browserLines`
`dataUrl`
`dbTrackType`
`fieldCount`
`firstItemPos`
`htmlFile`
`htmlUrl`
`initialPos`
`inputType`
`itemCount`
`mafFile`
`maxChromName`
`origTrackLine`
`tdbType`
`wibFile`
`wigFile`

Obscure or special case settings. (aka Rejections)

Rejected "types":

axt – rare bed 3 variant (replaced with netAlign?), panTro1.axtNetHg16

drosophila/dp1/trackDb.ra:type axt dm1

human/hg13/trackDb.ra:type axt mm3

human/hg15/trackDb.ra:type axt mm3

worm/ce1/trackDb.ra:type axt cb1

worm/ce2/trackDb.ra:type axt cb1

bedLogR – encode 1% test only??? Not found with tdbQuery from *

human/encodeTest/wgEncodeMetaCheckTest.ra

chromGraph - ??? Not found in tdbQuery -strict from *

gff http://genome.ucsc.edu/FAQ/FAQformat.html#format3

Not found in tdbQuery -strict from *

gtf http://genome.ucsc.edu/FAQ/FAQformat.html#format4

Not found in tdbQuery -strict from *

maf – replaced by wigMaf hg17, tdbQuery -strict: 1 track: fr1.tbaFishBirdCFTR

http://genome.ucsc.edu/FAQ/FAQformat.html#format5

net but not netAlign - custom only??? Not found with tdbQuery non strict

sample – RARE bed variant, hg15.affyTranscriptome, Affymetrix Transcriptome

hg15.hg15Mm3L

Completely replaced by type wig and more recently bigWig

List of Miscellaneous Specal Case, Deprecated, Rejected or Rarely Used Settings

Rejected settings	For Types	Reason
`accession`	all ENCODE only	ENCODE only; DEPRCATED (replaced with mdb )
`canPack <off/on>`	all	NOT FOR HUBS. Deprecated. Almost tracks can be displayed in the five standard visibilities. However on some track types such as wiggles, `squish` and `pack` offer no real advantage over `dense` and `full`. By default, these tracks will not offer the less valuable visibilities. Nevertheless, you can make your track offer these visibilility choices by turning canPack on. Note: subtracks of composites will always offer all five choices. Example: canPack on
`cdsDrawDefault`	genePred	There are a number of occurrences of cdsDrawDefault in our trackDbs, always set to ‘genomic\ codons ‘. However, I have found no documentation and no code that references this setting.
`cdsDrawOptions`	psl	I have found no documentation and no code that references this setting. Also, I do not see it in our trackDbs.
`cdsEvidence`	genePred	Used by JK experimental tracks only as either `jkgTxCdsEvidence` or `jkgTxCdsEvidence2`. This will show an evidence table named in the setting.
`cell`	bed, bedGraph ENCODE only	Obsolete: replaced with metaDb.
`chip`	expRatio, bed ENCODE only	DROP (no takers in any of our trackDb.ra files)
`dateSubmitted`	bedGraph, bed ENCODE only	Obsolete: replaced with metaDb.
`dateUnrestricted`	bed ENCODE only	Obsolete: replaced with metaDb.
`db`	chain, netAlign, genePred, bed 3	Not found in any of our trackDb.ras. Further, this is the same as assembly so implicit.
`dbProfile`	all	In hg18 experimental and cancerGenomics only.
`dividers`	all	OBSOLETE: use sortOrder instead.
`endFudge`	bed	Special case for hg17 HGSV Discordant (variation) tracks. Used in hgc to fudge chromEnd, I think.
`ensArchive`	genePred	Only in danRer4 Ensembl NonCoding to generate an Ensembl URL.
`ensemblTranscriptIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`ensemblGeneIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`ensemblIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`expProbeTable`	expRatio	Can't find code that supports this.Rare: only in human. affyHumanExon "Affy All Exon"
`extTable`	all	This setting points to a one record table that holds the external filename. This should be replaced by: track, table or bigDataUrl. (rare bigWig hg18.brTestPlus experimental track)
`extraFields`	bed	OBSOLETE: replaced by looking up "as" table description. However, that method does not allow for: selective inclusion/exclusion of fields reordering fields formatting titles
`filePos`	all	Can't find this in any of our trackDb.ra files.
`filterTopScorers`	bed5FloatScoreWithFdr, bed5FloatScore ENCODE only	Currently only used by pilot encode 1%. Presents user option to limit to the top scoring N items. Might be useful in other MySQL table based tracks but how valuable is it?
`gainColor` `lossColor`	bed ENCODE only	Currently only used by pilot encode 1% in hg17.encodeDless. Provides special color for "gain" and "loss" items.
`graphType`	bedGraph	Not found in code. Probably typo of graphTypeDefault. (rare hg18.encodeRegulomeDnaseArray)
`hgGene`	genePred	Cannot find code for this. No effect. ???
`informant`	genePred	Special setting for N-SCAN genes. Swapped into html description page.
`inputTracksSubgroupDisplay`	bed, factorSource ENCODE only	Only in hg18/hg19 wgEncodeReg*Clustered tracks. In code #ifdef TO_BE_REMOVED.
`itemAttrTbl`	genePred	Only used in borEut13. transMapRefGene.
`linesAt`	chromGraph	Unused track type (tdbQuery -strict).
`longlabel`	genePred	Typo, should be longLabel.
`longLabelClip`	all	Only used in sacCer3 (tdbQuery -strict).
`mafDot`	wigMaf	Can't find this in any of our trackDb.ra files and only supported as cart var.
`mafDotDefault`	wigMaf	Can't find this in any of our trackDb.ra files.
`mapDispatcher`	expRatio	Only hg17 group "x" [tingwang 2007] and not in C.
`maxScore`	broadPeak	Obsolete, replaced with scoreFilterLimits.
`metadata`	all ENCODE only	OBSOLETE: replaced by metaDb. Currently only way for datHubs to have metadata dropdowns. Used by WashU hubs.
`mgiUrl`	bed	Special case variant of url used by no current tracks (tdbQuery -strict).
`mgiUrlLabel`	bed	Special case variant of url used by no current tracks (tdbQuery -strict).
`minMax`	chromGraph	Unused track type (tdbQuery -strict).
`minScore`	bed, narrowPeak, broadPeak	Obsolete, replaced with scoreFilterLimits.
`msaTable`	wig, wigMafProt, wigMaf	Only hiv tracks use this. Code in wigMaf display and is used to look up species order.
`ncbiAccXref`	bed	Special case used by hg17/hg18 kiddEichler tracks. Names a table to convert kiddEichler IDs to NCBI IDs and print links.
`nextItemButton`	all	This setting lets you override the Browser wide setting to disable nextItem arrows (which is off by default). When this is on, the nextItem arrows will show up for your track. The opposite does not seem to be the case, where nextItems are enabled, but you want to exclude them from your track.
`noInherit`	all	This one should be OBSOLETE but there continue to be edge cases where this setting has some affect. Currently only 2 places this is read this: in hdb to makesuperChildren inherit settings from their supertrack. This is done by putting the super settings into the child's settings hash. tdbQuery where it appears to have no affect.
`nonBedFieldsLabel`	bigBed	OBSOLETE when bigBed has "as" definitions. Instead, the extraFieldsPrint should pick up the non-standard bed fields straight from the as definition.
`notNCBI`	bed	Only used in drosophila dm2/dm3. Referenced in hgc.c code.
`ococci`	bed	Not referenced in any of our trackDb.ra files or in code.
`otherOrg`	chain, netAlign	Typo: should be otherDb.
`onlyVisibility`	all	Not universally supported (rightClick/subtrack cfg, etc.) so deprecate or else expand. This setting restricts the visibility options of a track to only one setting such as "`full`". (rare hg19.lincRNAsAllCellTypeTopView)
`otherDbTable`	bed	Special case for Jackson lab's QTL (Quantitative Trait Locus) tracks.
`pairedEndUrlFormat`	bed	Special case only used on kiddEichler track. This is another external URL variant.
`pairwise`	wigMaf	Deprecate, replaced by summary.
`patDb`	expRatio	Only hg17 group "x" [jzhu 2007] and not referenced in C.
`patKey`	expRatio	Only hg17 group "x" [jzhu 2007] and not referenced in C.
`patTable`	expRatio	Only hg17 group "x" [jzhu 2007] and not referenced in C.
`pgDbLink`	bed	Special only used in hg18/hg19 Genome Variants so far. This setting is used to name one or more tables that hold links to phenotype and other databases for pgSnps. Each table must have chrom, chromStart, chromStop, name and srcUrl as fields. The links will be seen in the bed item details page and will be looked up in each listed table by item location. Example: pgDbLink pgKb1PhenCode pgKb1Snpedia pgKb1Hgmd
`private`	bed	Only used in human/hg7/trackDb.ra, and not even there using tdbQuery -strict. Prevents access to data by removing from trackList when doing "pruneEmpties". Gotta wonder when the track is ever seen in the browser or why it is a track at all.
`pslTable`	bed	Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same `illuminaProbesAlign` when track is "illuminaProbesAlign".) Used for making an hgcAnchor `htcIlluminaProbesAlign`.
`pubsArticleTable`	bed, psl	Special for publications track.
`pubsMarkerTable`	bed, psl	Special for publications track.
`pubsPslTrack`	bed, psl	Special for publications track.
`pubsSequenceTable`	bed, psl	Special for publications track.
`refSeqAnnoVersion`	genePred	Special for rheMac2.refSeqAnno track. Not found in code.
`scoreFilterMax`	bed, bedLogR, peptideMapping, bigBed	OBSOLETE: replaced by scoreFilterLimits
`searchMethod`	bed	Error. Should be part of searchTable stanza, not track stanza. TODO: Document searchTable stanza.
`searchType`	bed	Error. Should be part of searchTable stanza, not track stanza. TODO: Document searchTable stanza.
`selectSubject`	psl	Special only used in hiv(only used by hiv and h1n1. (Just h1n1 according to tdbQuery -strict).
`seqTable`	bed	Special for hg18/hg19 illuminaProbes "Illumina WG-6". Used in hgc. (Hardwired to be the same `illuminaProbesSeq` when track is "illuminaProbesAlign".) Used for making an hgcAnchor `htcIlluminaProbesAlign`.
`settingsByView`	all	OBSOLETE: replaced with "view in the middle" view as separate track.
`snpTable <table>`	bed gwasCatalog only	Special for gwasCatalog: table used to map dbSNP IDs to genomic coords
`snpVersion`	bed gwasCatalog only	Special for gwasCatalog: dbSNP build number of table used to map dbSNP IDs to genomic coords
`speciesTarget`	wigMaf	OBSOLETE. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with `#define BRANEY_SAYS_USETARG_IS_OBSOLETE.`
`speciesTree`	wigMaf	OBSOLETE. Replaced by treeImage. Not in our trackDbs (tdbQuery -strict). Specifically ifdef'd out of code with `#define BRANEY_SAYS_USETARG_IS_OBSOLETE.`
`speciesUseFile <fileName>`	wigMaf	Deprecated Much more rarely used, this setting can replace `speciesOrder` and `speciesGroups`. Set the `speciesUseFile` to a path relative to the apache cgi-bin. The file should contain a single species name as the first word of each line. Example: speciesUseFile speciesLists/conserved8Way.txt
`stripPrefix`	bam	Not yet implemented? Only on hg18.oneKGHighCovSeq experimental track.
`subgroups`	bed	Typo: should be subGroups.
`subTrack`	all	OBSOLETE: replaced with parent.
`symbolTable`	bed, genePred	In hgTracks, flyBaseGeneName() methods, if an item name is found in this symbol table, the symbol name will be shown instead. Found in drosophila and strangely rn4 RGD Genes (but table named in rn4 does not have a symbol column. Instead, symbol lookup is hard-coded to rgdGene2ToSymbol).
`txInfo`	genePred	Only seems to be used in experimental tracks in hg18 and mm8.
`urlName`	genePred	Not referenced in code and rarely used. (e.g. hg18: encodePseudogeneConsensus, encodePseudogeneYale).
`url2`	bed	Special cased second URL used much like url.
`url2Label`	bed	Special cased second URL label used much like urlLabel.
`useScore`	bed, factorSource, bed5FloatScore, broadPeak	Deprecate: replaced with spectrum as a slighly less obscurely named setting.
`vegaGeneIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`vegaTranscriptIdUrl`	genePred ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`visibilityViewDefaults`	all	OBSOLETE since view in the middle change. LOSE
`wgEncodeGencodeVersion`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeAttrs`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeExonSupport`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeGeneSource`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTranscriptSource`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodePdb`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodePubMed`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeRefSeq`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTag`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTranscriptSupport`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeUniProt`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodePolyAFeature`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeAnnotationRemark`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`wgEncodeGencodeTranscriptionSupportLevel`	genePred ENCODE Gencode Only	Special for ENCODE Gencode.
`yLinOnOff`	wigMaf	Typo: should be yLineOnOff.
`yalePseudoAssoc`	all ENCODE Gencode Only	Special for ENCODE Gencode.
`yalePseudoUrl`	all ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.
`yaleUrl`	all ENCODE Gencode Only	Special for ENCODE Gencode to generate external URL.

Track Database Definition

How to declare Dataset Display Settings in the Genome Browser

Hub contributors should use the Hub Track specific version of this document.

This document describes how to declare dataset display characteristics in the Genome Browser through trackDb settings. Introducing new datasets for display in the Browser requires declaring the location and format of the data and defining initial display characteristics. In many cases, you may need to choose how the displayed data (aka "track") may be selected and configured. These settings are declared in a simple text file format and stored in a database called the "track database", or trackDb for short.

The text file format for trackDb settings follow the simple "ra" rules which establish a "record" as a set of related settings in a "stanza" delimited by blank lines. The first line of each stanza typically establishes the "key". Each line in a stanza will contain a single word "setting" name and one or more words or numbers that follow are the setting's "value". All trackDb stanzas are keyed by "track" and most will have certain common settings followed by track specific settings. Here is an example:

        track myFirstTrack
        type bed 6
        shortLabel Example Data
        longLabel The data in this track is format "bed 6".

Every track should have these four settings. The key of this track (myFirstTrack) is the name of the dataset. If the data is loaded into a MySQL table then the track name is almost always the table name. If the data is in one of the remote indexed file types (e.g. bigWig, bam, etc.) then the name is typically the root file name. However, this is a key to the track so it must be unique within the Genome Browser. (Data hubs need only declare track names unique to their hub.) After the "track" key, the most important setting for defining a track is the "type". This tells the Browser which format the data is in, defines how to display it, and determines which options are available for fine control of that display.

Hub Track Database Definition

How to declare Dataset Display Settings in Genome Browser Hubs

This document describes how to declare dataset display characteristics in a Genome Browser Hub through trackDb settings (please note that hosting hub files on HTTP tends to work even better than FTP). Introducing datasets for display in the Browser requires declaring the location and format of the data and defining initial display characteristics. In many cases, you may need to choose how the displayed data (aka "track") may be selected and configured. These settings are declared in a simple text file format and loaded into the Browser's "track database", or trackDb for short.

        track myFirstTrack
        type bigBed 3
        bigDataUrl myFirstTrack.bb
        shortLabel Example Data
        longLabel The data in this track is format "bigBed 3".

Every hub track should have these five settings. The key of this track (myFirstTrack) is the name of the dataset and is typically the root file name. However, this is a key to the track so it must be unique within your data hub. After the "track" key, the most important setting for defining a track is the "type". This tells the Browser which format the data is in, defines how to display it, and determines which options are available for fine control of that display.

The following settings, which must be defined for each trackDb record, are common to all data format types. The first few settings are required for all tracks. Some type-specific requirements will be mentioned in the appropriate sections to follow.

track

Required: Yes

This is the name of the dataset and must be unique within the Genome Browser or dataHub. Typically this is the MySQL table name or remote data file root name (without path or suffix). Must begin with a letter and contain only the following chars: [a-zA-Z0-9-_].

Example:

   track myFirstTrack

type

Required: Yes

Declares the format of the data and is used to determine display methods and options.

Valid settings:

altGraphX, bam, bed, bed5FloatScore, bedGraph, bedRnaElements, bigBed, bigWig, broadPeak, chain, clonePos, coloredExon, ctgPos, downloadsOnly, encodeFiveC, expRatio, factorSource, genePred, gvf, ld2, narrowPeak, netAlign, peptideMapping, psl, rmsk, snake, vcfTabix, wig, wigMaf

Detailed descriptions of each type can be found below. In many cases the type setting includes additional parameters to further specify the data format. Some track types have additional setting requirements, to be discussed below.

Example:

   type bed 6 +

type

Required: Yes

Declares the format of the data and is used to determine display methods and options.

Valid settings:

bam, bigBed, bigWig, vcfTabix,

Example:

   type bigBed 6 +

shortLabel

Required: Yes

Specifies the track's "short label", which is used in a number of places in the Browser to identify the track. For example, the short label is displayed alongside the track in the Browser image. This label must be brief and is limited to 17 printable characters.

Example:

   shortLabel Human mRNAs

longLabel

Required: Yes

Specifies the track's "long label", which is also used in numerous places in the Browser to identify a track. For instance, the long label is displayed above the track's data in the Browser image. This label should be descriptive enough to allow users to uniquely identify the track within the Browser. It is limited to 76 printable characters.

Example:

   longLabel Human mRNAs from GenBank

visibility

Required: No

Visibility (i.e. "display mode") specifies which of 5 modes (including 'hide') should be used to display the track within the Browser image. This setting is almost always dynamically customizable by each user. The exact configuration of the display for each mode depends upon the track's type, and some modes may not be supported for certain track types. Be sure to experiment with this setting to verify that it works as expected for your track type.

Valid settings:

hide: DEFAULT. The track is not displayed in the Browser image unless the user changes the display setting.
dense: The track is displayed as a single line or ribbon. In many cases multiple items are summarized or drawn on top of one another, and the long labels are not displayed.
squish: Each item is drawn individually, but at half height and without a label. (Not supported for all types.)
pack: Items are displayed individually at full height, but in a much more compact vertical space than in full mode. (Not supported for all types.)
full: Each item is displayed as a separate line in the Browser image. Graphed signals may be displayed in varying heights.

Example:

   visibility dense

html

Required: No

Specifies a file that contains the complete description of a track in HTML format. The path of this file name is relative to the path of the trackDb file. The ".html" suffix is implied.

To be consisent with standard Genome Browser track descriptions, this description should contain several sections:

Description

A few sentences describing the contents of the track and what it attempts to show. The description can include additional paragraphs giving further details and can include links to outside sources.

Display Conventions and Configuration

A description of what the display represents. This includes a description of conventions for coloring and any special glyphs used in the track. It may describe how to interpret scores or full signal values. This section can also be used to describe how to customize the display by using configuration controls.

Methods

A description of how the data was generated, which may include how physical samples were treated as well as explanations of data-handling algorithms.

Credits

Names and institutions of those who performed the experiments and/or prepared the data as well as any funding sources. This section should include a contact email address for questions concerning the data.

References

References to any published work referring to or dependent upon this data as well as any sources upon which the work is based or can be understood.

Example:

    html docs/myFirstTrack

Common, though less frequently used settings

The following settings are available for many or all track types but are less frequently used. Most are optional, but some may be required for specific track types or in specific situations.

Inside hint: The ra file format supports '\' continuation characters. If the setting is long or complex, break it into several lines using terminating '\' characters to make it more readable.

bigDataUrl <url/relativePath>

Required: For Hubs

The location of a remote data file containing the bulk of the data for the track. This setting is required for all data tracks in a track hub. It is currently not supported for local tracks.

The setting is either the full URL (including http: or another protocol) or it is relative to the directory in which the trackDb file containing this setting is located. The file must be in one of the supported remote data file formats: bam, bigBed, bigWig or vcfTabix. Note that bam and vcfTabix types require a separate index file that must have the same name as the data file plus a standard suffix (".bai" and ".tbi" respectively).

Example:

   bigDataUrl http://vizhub.wustl.edu/VizHub/hg19/biBrainH3K4me1.bb

   bigDataUrl biBrainH3K4me1.bb

boxedCfg <on/off>

Configuration controls can be placed inside a box on the configuration page. This setting is decorative only, but can make a busy page look more cohesive. Not all track types currently support this feature, but the most common types do, including wig, bigWig, bed, and bigBed. DEFAULT: off.

Example:

   boxedCfg on

canPack <off/on>

NOT FOR HUBS. Deprecated.

Most tracks can be displayed in all five visibilities modes. However on some track types such as wiggles, the squish and pack modes offer no real advantage over the dense and full modes. By default, these tracks will not offer the squish and pack vilibility settings. Nevertheless, you can make your track offer these visibilility choices by turning canPack on. Note: subtracks of composites will always offer all five choices.

Example:

   canPack on

color <red,green,blue>

Many track types allow the color of the data displayed in the image to be specified with this setting. The setting accepts red, green and blue values, each in the range of 0-255 and delimited by commas. Though this setting is widely supported, some track types in certain display modes ignore it, such as the EST tracks in dense mode.

Example:

   color 255,0,0

This example sets the color to red.

altColor <red,green,blue>

Many track types allow setting a color range that varies from color to altColor. For instance the CpG Island tracks use the altColor setting to display the weaker islands, while the stronger ones are rendered in color. If altColor is not specified, the system will use a color halfway between that specified in the color tag and white instead.

Example:

   altColor 0,0,255

This example sets the alternate color to blue.

chromosomes <chr1,chr2,...>

Some datasets do not contain data for all chromosomes of a genome. When this is true, use this setting as a comma-separated list of the chromosomes that are covered. The system displays a message that no data is available when the user browses chromosomes not included in this list.

Example:

   chromosomes chr1,chr7,chr18,chr19,chr22,chrX,chrM

configureByPopup <on/off>

NOT FOR HUBS.

Most track displays that can be configured by a user can also be configured from directly within the Browser image through a right-click option that pops up a configuration dialog. While this functionality works on the majority of track types, some configuration dialogs are too complex or have too much embedded javascript control to be reliably configured through a pop-up. To turn off the ability to configure the track via right-click, change this setting to "off". The user will still be able to configure the track on the track's configuration page. DEFAULT: on.

Example:

   configureByPopup off

dataVersion <str>

Many tracks undergo multiple revisions over time. In some cases, the older versions should be retained, but even if they are not, it can be useful to declare the current version of the track. Use this setting to display a version statement on the track configuration page and item details page of a track. The string will support limited HTML.

Example:

   dataVersion May 2011 <em>beta</em>

Related settings:
directUrl <url>

By default, items shown in the Browser image can be linked to a details page giving information about that item. The link can instead go to the URL declared here. The URL is formatted as a printf line including the following fields in this order:

%s - item name
%s - chromosome name
%d - chromosome start position (relative to zero)
%d - chromosome end position (relative to one)
%s - track name
%s - database name

Not all fields need be present, but those present must be in this order, and if a later field is present, all earlier fields must be used. The URL can either be a full external URL or local to the web site.

Examples:

   directUrl http://mygenes.org/cgi-bin/geneView/%s

   directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s

hgsid on

NOT FOR HUBS.

The "cart" is a hidden table that contains the persistent selections that users have made in the Genome Browser. To ensure your directUrl has access to these cart settings, include the user's Browser ID with this setting.

Example:

    directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s
    hgsid on

In this example the URL specified by directUrl will have the user's Browser ID appended so that cart settings will be available.

iframeUrl <url>

This setting allows integrating an external html page into the default details page, as an iframe. The usual replacement variables can be used within this URL:

$$ - ID, will be replaced by the name of an item or other string id depending upon the fields in the given track's type.
$T - database table name
$S - chromomosome name (scaffold name on scaffold assemblies)
$[ - chromStart location (relative to zero)
$] - chromEnd location (relative to one)
$s - chromosome name without chr prefix (or without scaffold_ or Scaffold_ prefix on scaffold assemblies)
$D - database name (e.g. "hg19")
$P - item name portion before first : in name
$p - item name portion after first : in name up to next colon

The URL can either be a full external URL or local to the web site.

In HTML, iframes cannot be resized easily, so the default static size is 1024 pixels. This can be changed with iframeOptions

Examples:

    iframeUrl http://www.ncbi.nlm.nih.gov/nuccore/$$
    iframeOptions height='600' width='1024'

iframeOptions <string>

When iframeUrl is used, this statement specifies a string that is inserted literally into the HTML <iframe> tag. It can include options needed for iframe formatting, like width, height, scrolling, etc.

If the statement is not present, the default is width='100%' height='1024'.

Note: dynamic resizing of iframes is not trivial, as they have to be resized with javascript, across domains. We recommend keeping the size static and to use scrollbars. If dynamic resizing is required, the iframed page has to include a few lines of special HTML and javascript code and one has to modify its body-tag, like this (see stackoverflow):

    ... html header ...
    <body onload="iframeResizePipe()">
    <iframe id="helpframe" src='' height='0' width='0' frameborder='0'></iframe>
    <script type="text/javascript">
      function iframeResizePipe() {
       var height = document.body.scrollHeight;
       var pipe = document.getElementById('helpframe');
       pipe.src = 'http://genome.ucsc.edu/inc/iframeHelper.html?height='+height+'&cacheb='+Math.random();
      }
    </script>
    ... rest of webpage ...

Example:

   iframeOptions width='800' height='800' scrolling='yes'

This example fixes the size to 800x800 pixels and activates scrollbars.

directUrl <url>

%s - item name
%s - chromosome name
%d - chromosome start position (relative to zero)
%d - chromosome end position (relative to one)
%s - track name
%s - database name

Example:

   directUrl http://mygenes.org/cgi-bin/geneView/%s

otherDb <otherDb>

Track types that show pairwise alignments often need to declare the other species/assembly included in the alignment. Types that use this setting include bed, chain, netAlign, psl and snake.

Example:

   otherDb mm10

This example sets the second assembly in the alignment to the mouse mm10 assembly.

origAssembly <db>

NOT FOR HUBS.

The original assembly version for which the dataset was generated. Datasets generated by mapping to one genome assembly may prove useful enough to map to a more recent assembly. Ideally datasets will be regenerated to map to the new assemblies coordinates, but sometimes this is not practical or expedient. Therefore, the dataset may have its genome coordinates "lifted over" to the more recent assembly. In some cases this results in an inferior but nevertheless useful representation. Such datasets should have their original assembly defined with this setting.

Example:

   origAssembly hg18

pennantIcon <icon> [html [tip]]

Certain tracks can be visually flagged in the Browser by use of an icon and a link to a description of the icon's meaning. The icon is displayed next to the track's short label in the track groups section below the Browser image, and on the track's description and configuration pages. This setting has three parts:

icon - Currently must refer to an icon in the Browser's images directory in the Browser source tree.
html - A relative or full html path to a description document explaining the icon's meaning. This page displays when the user clicks on the icon.
Tip - A "quoted string" tip that will be seen when the user's mouse pointer hovers over the icon.

Example:

    pennantIcon 18.jpg ../goldenPath/help/liftOver.html "lifted from hg18"

priority <float>

The priority is used to define the order of a track within its track group or data hub, as well as its default order within the Browser image. The order within the image can be dynamically changed by the user and will always depend upon which other tracks are currently visible. Typically the priority is set only for tracks that are on by default in order to move them ahead of other tracks. Prioritized tracks within a group or data hub are displayed in ascending priority order, followed by unprioritized tracks sorted alphabetically by short label. Tracks of the same priority within a group or hub are sorted by short label. Priority is a floating point number. Default: 0.

Example:

   priority 50

release <alpha/beta/public>[,beta/public]

NOT FOR HUBS.

This specifies the version of the Browser where the track will be displayed. It can contain any combination of the three values:

alpha - displayed on the alpha Browser (aka genome-test, hgwdev)
beta - displayed on the beta Browser (aka hgwbeta)
public - released on the public Browser (aka genome.ucsc.edu)

Default: alpha,beta,public (all three Browsers).

Example:

   release alpha,beta

table <tableName>

NOT FOR HUBS.

The track setting of most tracks is the same as the table name. However, in some cases it is desirable to reference the same table in more than one track. An example of this is showing a table as a single signal track and as part of a combination overlay track, as described later in this document. For data contained in MySQL tables, this setting must be used if the track setting is not the name of the table.

Example:

    track mySecondTrack
    table myFirstTable

tableBrowser <off/on> [table1 ...]

NOT FOR HUBS.

The Table Browser typically allows querying and downloading of some or all of the raw data for a track. This setting can be used to block Table Browser access to datasets with restrictions (for example, those with confidentiality or licensing limitations). By naming additional tables in this setting, access to those tables can be denied as well.

Example:

   tableBrowser off decipherRaw knownToDecipher

The table for this track, as well as the decipherRaw and knownToDecipher tables, are blocked from Table Browser access.

url <url>
urlLabel <label>
idInUrlSql <sql for id>

Many tracks allow an external link when an individual track data item is examined. Use this setting to put a link to an external URL on the details page. The url may include wildcards that will be substituted with values from the track data or other Browser variables:

$$ - ID, will be replaced by the name of an item or other string id depending upon the fields in the given track's type.
$T - database table name
$S - chromomosome name (scaffold name on scaffold assemblies)
$[ - chromStart location (relative to zero)
$] - chromEnd location (relative to one)
$s - chromosome name without chr prefix (or without scaffold_ or Scaffold_ prefix on scaffold assemblies)
$D - database name (e.g. "hg19")
$P - item name portion before first : in name
$p - item name portion after first : in name up to next colon

The default prompt the user will see for this url is "outside link:". Use urlLabel to provide a more informative prompt.

For local (non-hub) tracks, an additional setting can be used to find an ID from another table based upon the item name or id from the track's table. The value found will replace the "$$" token in the url. Note that the format of this trackDb setting is a normal C language format so that the item will replace the "%s" token in the sql statement.

Example:

    url http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$
    urlLabel NCBI Details:
    idInUrlSql select name from sibTxGraph where id=%s

url <url>
urlLabel <label>

$$ - ID, will be replaced by the name of an item or other string id depending upon the fields in the given track's type.
$S - chromomosome name (scaffold name on scaffold assemblies)
$[ - chromStart location (relative to zero)
$] - chromEnd location (relative to one)
$s - chromosome name without chr prefix (or without scaffold_ or Scaffold_ prefix on scaffold assemblies)
$D - database name (e.g. "hg19")
$P - item name portion before first : in name
$p - item name portion after first : in name up to next colon

The default prompt the user will see for this url is "outside link:". Use urlLabel to provide a more informative prompt.

Example:

    url http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$
    urlLabel NCBI Details:

urls <fieldName1>="<url1>" <fieldName2>="<url2>" ...

This is similar to the url tag, but allows urls on fields that are not the "name" field. Use this statement if you need multiple linkouts on the details page or if your linkout is not based on the name field.

Put the identifiers for these links into extended bigBed fields as explained in example 3 of the bigBed documentation. The field names from your .as file are the field names referenced in this statement. The urls in this statement support the same wildcards as the url statement. Make sure to enclose the URLs in double quotes. The default label for the identifier is the field description in the .as file (all text after the # mark).

Example:

    urls pmid="http://www.ncbi.nlm.nih.gov/pubmed/$$" hgncId="http://www.genenames.org/data/hgnc_data.php?hgnc_id=$$"

mouseOverField <fieldName1>

For bigBed files with more than 8 fields, this adds mouse over text that are different from the "name" field of a bigBed file. If the field is empty then the mouse over will fallback to the name field.

To make this work, create a bigBed file with at least 8 columns and put the text for the mouse over into extended an bigBed field as explained in example 3 of the bigBed documentation. The field name from your .as file is the field name referenced in this statement.

Example:

    mouseOverField comment

wgEncode on

NOT FOR HUBS.

This setting designates an ENCODE track. It activates the following special features:

Special thumbnail (NHGRI helix) is displayed before the track label in the brower track menu
ENCODE logo is displayed on track configuration page
'Downloads' and 'Preview' browser links shown in upper right portion of track configuration page
Track description includes a note about data on preview browser
'downloads' and 'metadata' links appear after 'View table:' on track details page

Example:

   wgEncode on

bed/bigBed: Item or region tracks

Some of the most common track types are those that highlight regions or items of varying size in a genome assembly. There are many variations to the "items" track, most of which are specified with a bed or bigBed format. These two formats are really a cluster of many formats all starting with three common fields (chromosome start end) and having optionally many more fields. For complete bed or bigBed format definitions please see the FAQ.

bigBed: Item or region tracks

Some of the most common track types are those that highlight regions or items of varying size in a genome assembly. There are many variations to the "items" track, most of which can be represented with a bigBed format. This format is really a cluster of many formats all starting with three common fields (chromosome start end) and having optionally many more fields. For complete bigBed format definitions please see the bigBed help page.

type bed <3-12> [+/.]
type bigBed <3-12> [+/.]

Both bed and bigBed declare the number of standard bed fields in the data. Additional fields may follow these standard ones. If so, the type should end with a '+' (plus). Even if there are not additional non-standard fields, the additional parameter '.' (dot) is needed, if this track is meant to be configurable.

Examples can be found below.

type bigBed <3-12> [+/.]

Type bigBed declares the number of standard "bed" fields in the data. There may be additional fields following these standard ones. If so, the type should end with a '+' (plus). Even if there are no additional non-standard fields, the parameter '.' (dot) must be specified if this track is meant to be configurable.

Examples can be found below.

type bed5FloatScore
type bedRnaElements
type broadPeak
type coloredExon
type gvf
type ld2
type narrowPeak
type peptideMapping

Each of these is a specialized variation of the bed format. Their specialized definitions should be sought elsewhere. However, these item tracks share many of the same configuration options available to bed tracks.

An example can be found below.

bigDataUrl <url/relativePath>

This setting is for remote data file type tracks (e.g. bigWig) and is fully described in the "Common trackDb settings" portion of this document.

colorByStrand <red,green,blue> <red,green,blue>

To color items differently by the strand they align to, use the colorByStrand setting. The first color will be used for plus strand alignments and the second for the minus strand. This setting is incompatible with spectrum and all items on the same strand will have the same color, regardless of the item's score.


    Example:
       colorByStrand 255,0,0 0,0,255
    Plus strand alignments will be colored red, and minus
    strand alignments will be blue. This setting is incompatible with spectrum, 
    and therefore all items on the same strand will have the same color, regardless of the item's
    score.




compareGenomeLinks <db[.table[.column]]=label>
            [db[.table[.column] =label …]
    NOT FOR HUBS
    Sometimes the
    features that a bed track highlights in one genome are also
    displayed in tracks of other genomes.  If an item of the same name
    exists in the bed tracks of two or more genomes, a bridge can be
    readily made between them through links on the item's detail page. To establish
    this association, the feature must have the same name in each genome, and the name 
    must be unique within the bed track of each genome.  The components of this
    setting are a genome assembly database, an optional table and column,  
    with a label for the link.  If the column parameter is omitted, it is
    assumed to be name. If the table is omitted, it
    is assumed to be the same as the current table.  Links to multiple
    genomes can be established with this setting, as each pair is
    joined by '=' and delimited by space.  Be sure to use
    '_' as a substitute for spaces in the labels.
    Example:
        compareGenomeLinks panTro2=Chimpanzee_(March_2006) rheMac2=Rhesus_(January_2006) \
                       mm9=Mouse_(July_2007) rn4=Rat_(November_2004) canFam2=Dog_(May_05) \
                       bosTau4=Cow_(October_2007)    
    In this example for
    the hg18 ENCODE bi-directional promoter track, each genome has a
    track of the same name, and the names are unique within each track.
    However, a named bi-directional promoter will not be found in
    every genome; therefore, only links to genomes where the name is actually
    found will be displayed.
    




denseCoverage <maxVal>
    bigBed specific
    Type bigBed tracks
    in dense mode do a density plot based on maximum coverage seen at
    each pixel.  The maxVal corresponds to the count at which the plot
    reaches maximum darkness.  If maxVal is 0 then this will be
    calculated from the data itself.
    Example:
       denseCoverage 100



exonArrows <on/off>
    On tracks that show
    exons or blocks within features, exon arrows allow the user to jump to
    the next exon or block outside the image. Exon arrows are typically shown by default
    in these types of tracks, with the exception of tracks in the Regulation group. 
    The arrows can be explicitly shown or hidden using this setting.
    
    Example:
       exonArrows off




    <column>Filter <low>[:<high>]

    scoreFilter <low>[:<high>]

    pValueFilter

    qValueFilter

    signalFilter

    <column>FilterLimits <low>[:<high>]

    <column>FilterByRange <off/on>
    
    NOT FOR HUBS.  Not yet supported by bigBeds
    A number of
    numerical filters are available for bed tracks.  These are
    conveniently named by the field that is filtered on.  The most
    common numerical filter is based on the standard bed field
    score, and is thus controlled by the scoreFilter
    setting.  Other examples are pValueFilter, qValueFilter and
    signalFilter, which are filters on non-standard bed fields defined
    in the broadPeak and narrowPeak formats.  These numerical filter
    settings should include the default value.  If the numeric field
    is floating point, the default should contain at least one decimal
    place.
    
    By default the range
    of values for a numeric filter is 0 to 1000.  However, you
    can explicitly set the upper and lower limits of the filter by
    setting <column>FilterLimits.
    
    The numeric filters
    will exclude items that fall below the setting. That is, a
    scoreFilter of 800 will  exclude all items with a score below 800.
    You can also filter for values within a range, by including the
    <column>FilterByRange setting.  For example, a 
    scoreFilter range of
    800-900 will include only items with scores at or above 800 and
    below 900.
    Note: multiple
    filters of different fields are allowed.
    Examples:
       scoreFilter 100
    In this example, the standard bed
    field score, which is an integer, will be used to filter items
    in the track.  By default, items with scores below 100 will be
    excluded.  Also by default the limits of the scoreFilter are
    0-1000.
        pValueFilter 3.0:15.0
    pValueFilterLimits 0.0:15.0
    pValueFilterByRange on    
    The non-standard bed field pValue, which
    is floating-point, will be filtered by range.  The expected data
    range is 0.0 to 15.0, and by default only items with pValues within the 3.0 to 15.0
    range will be displayed.




    scoreFilter <low>[:<high>]

    scoreFilterLimits <low>[:<high>]

    
    Type bigBed tracks can be filtered on the standard bed field
    score.  This numerical filter is requested by the 
    scoreFilter setting, which should include the default value.  
    
    By default the range
    of values for a score filter is from 0 to 1000.  However, you
    can explicitly set the upper and lower limit of the filter by
    setting scoreFilterLimits.
    
    The score filter will exclude items that fall below the setting. That is, a
    scoreFilter of 800 will exclude all items with a score below 800.
    Example:
        scoreFilter 300
    scoreFilterLimits 200:1000
    The standard bed
    field of score, which is an integer will be used to filter items
    in the track.  By default, items with scores below 300 will be
    excluded.  The filter cannot be set to less than 200 or more than 1000..



filterBy  <field1:title=[+]opt1a...>
                            [field2:title=[+]opt2a...]
    
    NOT FOR HUBS.  Not yet supported by bigBeds
    Another method of
    filtering items relies upon discrete values.  One or more fields
    such as name or score may contain a limited number
    of discrete values that can be filtered on. These discrete values will be
    displayed in a dropdown list from which the user can choose one or
    more options.  While the maximum number of options in the list is
    not limited, displaying too many options can be confusing for the user.
    
    Setting complexities:
    
     Because filters for different fields are delimited by whitespace, any
    whitespace in titles and labels should be replaced by the '_'
    (underscore) character.
     Each field/option pair is joined by '=' (equal sign).
     The field portion
    can have a title that is delimited from the field name by ': (colon)'.
     A single field
    filter will have multiple options delimited by commas.
     If the options are
    a 1-based index (1,2,3...) then the option list can be preceded
    with a '+' (plus sign) and the options themselves are only labels.
     Otherwise, each
    option will be a value and optional label delimited by '|' (vertical bar).
    Note that if one option has a label then all options of that filter
    must have a label.
    Finally,
    options may have CSS style wrapped in {curly} brackets and
    appended to the end.
    
    Because of this
    complexity, please remember to use the '\' continuation line to
    ensure the setting is readable:  
    
        filterBy {field1}[:{Title1}]=[+]\
             option1a[|label1a[{style1a}]],\
             option1b[|label1b[{style1b}]],... \
             [{field2}[:{Title2}]=[+]\
             option2a[|label2a[{style2a}]],,...]    
    It is probable
    that this setting will be redefined at some point, given that it
    is very complicated. However, this current format will
    be supported until entirely replaced.


    
        Secret tricks:
        
        Avoid the use of the delimiter chars  ,|:={} in titles and
        labels.  (These characters can be included via HTML codes.)  
        Spaces can be included by using the '_' character.
        The option labels
        can be in color or have other CSS style attributes. Append the style 
        enclosed in curly brackets and containing no spaces. For example:
        Pull_Over{color:#AA0000;text-decoration:blink;}.
        If one option has CSS style, then all options of that
        filter must include a style definition.
        The filterBy option is implemented in the code using an SQL where clause.
        For instance, filtering on the name field for "Fred" and
        "Ethyl" would result in an SQL where clause of
        "where name in ('Fred','Ethyl')".  In type genePred
        tracks, this knowledge is used to define filters on fields in a separate table!
        This is done by defining the field as {otherTableName}.{fieldName}.
        
    
    The best way to
    understand this setting is with an example.  This is an operational
    example in the hg19 "Open Chrom Synth" track.
    Example:
        filterBy color:Validation_Level=\
             0|Validated_(OC_1){color:#000000},\
             255|Open_Chromatin_(OC_2-3){color:#0000FF},\
             39168|DNase_low_(OC_2){color:#009900},\
             10027008|FAIRE_low_(OC_3){color:#990000},\
             16711935|ChIP-seq_(OC_4){color:#FF00FF} \
             ocCode:OC_Code=+\
             One&#58;_Validated_(all),\
             Two&#58;_DNase_(all),\
             Three&#58;_FAIRE_(all),\
             Four&#58;_ChIP_(all)    
    This setting sets up
    two filters, one on the field "color" and a second for the
    "ocCode" field.  The color filter is given the title "Validation
    Level".  The second option has a value of "255" and a label
    of "Open Chromatin (OC 2-3)".  Note that it will appear
    as blue in the list due to the {color:#0000FF} style definition.
    Also notice that all options for this color field have a style
    defined, even though the first option is black and would be so by
    default. In this example, the only
    whitespace within the setting value section immediately precedes the second filter
    definition.  The second filter, "ocCode", is titled by the
    inscrutable "OC Code".  It is a numeric index filter
    (as declared by the '+').  The value of the second option is 2 and
    only the label gets defined as "Two: Dnase (all)".  Note
    that the colon in the label is an HTML code.
    
    The filterBy setting is very powerful. We recommend that you experiment with the
    settings to determine which work best for your case.
    



itemRgb on
    In bed formats supporting 
    at least 9 standard bed fields, this setting can be used to activate
    item coloring using the value in the ninth field, itemRgb. The
    value of the  item field must be an R,G,B triplet.  When loaded
    into a table, this field appears as an integer with the RGB values
    in specific bits of the integer.
    Example:
       itemRgb on



maxItems <integer>
    Maximum number of items to display individually in full mode.  When the maximum is
    exceeded, the excess items are drawn on top of one another on the last line.
    In packed mode this refers to the number of lines rather than number of items.
    Default: 250. For type bigBed tracks, this setting can never 
    be larger than than 100,000.
    Example:
    
       maxItems 25



maxWindowToDraw <integer>
    When too many individual bed items are shown in the Browser image (such as 
    might occur when a large region of a chromosome is viewed), the
    information is often better visualized as a summary in dense mode.  
    Depending on the current visibility of the
    bed track and which other tracks are being shown concurrently, the
    Browser may automatically reduce the display to pack or dense mode.  This setting
    allows you to force the data summarization at whatever display limit you consider
    reasonable. Unlike the maxItems setting, which controls the display of
    vertical space, this setting dictates the number of bases to be displayed horizontally 
    in a window before the track is forced into dense mode.  There is no default for this 
    setting, but the maxItems setting will ultimately prevent too many items from
    being displayed.
    Example:
       maxWindowToDraw 200000
    Browser images that show more then 200,000 bases will result in the track being 
    displayed in dense mode.



minGrayLevel  <1-9>
    When a bed track contains the standard
    field score, and when that score is used
    to present items in gray or color scale (see
    spectrum),
    this setting specifies the lightest shade to be used.
    This prevents the lowest scores from being displayed in too light of a color to easily
    view. Set the value in the range 1 - 9, lightest to darkest.
    Example:
       minGrayLevel   4
    This sets the lowest scores to slightly
    less than medium gray, while the highest scores appear black.



noScoreFilter  on
    By default, bed
    tracks with 5 or more standard bed fields that contain either a '.' or
    a '+' in the type setting will be filterable on score;
    that is, they will have an assumed setting of "scoreFilter 0".  To turn
    this old-style default off, include the "noScoreFilter" setting.
    
    Example:
        type bigBed 6 +
    noScoreFilter on    




    spectrum on

    scoreMax <integer>

    scoreMin <integer>
    Replaces useScore.
    If your track is a
    bed 5 or greater, then the standard bed score
    field exists.  This score, which is expected to vary from 0-1000,
    can be used to control the shading of bed items drawn in the Browser
    image.  To activate this feature, set spectrum on.
    Lower scores will be shaded in light gray by default, while higher
    scores will trend towards black.  This can be modified in a number of ways:
    
     color
    can be used to replace gray scale with a color scale
     altColor
    with color can vary items from
    color to altColor
    minGrayLevel
    can be used to set the level of the lightest shade
     scoreMin
    and scoreMax can be used to define the lower and upper limits of 
    the range that will receive graded shading
    
    Example:
        spectrum on
    scoreMin 700
    scoreMax 900
    color 0,0,128    
    In this example, the track items will be
    displayed in blue. Items with scores less than or equal to 700 will be shown in very 
    light blue,
    those with scores between 700 and 900 will display in increasingly darker shades of blue, 
    and items
    with scores greater than or equal to 900 above will display in dark blue.



searchIndex <str>
     Specifies the list of field names on which a index has been made.
    When a user enters a string in the position search box of the browser,
    this index will be searched to find that name, and if the string is in 
    the index, the user will either be navigated to that position in the 
    browser, or if there are more than one matches of that string, 
    will be give a list of the positions to choose from. See HERE
    for instructions on how to build an index for a bigBed file.
    
Example:
       searchIndex name



searchTrix <url/relativePath>
     Specifies the URL to a TRIX file that maps free text to
    a set of indices that are assumed to have indicies in the associated
    bigBed file.  See HERE for instructions on how to build a TRIX file.
    
Example:
       searchTrix url or relative path 




thickDrawItem <off/on>
    In bed tracks that
    have 8 or more standard bed fields, portions of items in tracks such as
    gene models can be drawn thicker to differentiate exon regions from introns.
    When data is displayed at different scales, the items and the thick
    portions of the items should scale proportionally.  However, it
    may be more important to see the existence of the thick regions
    than it is to attempt to maintain the proportion.  By setting
    thickDrawItem on, the thick display regions of items are always drawn at a minimum 
    of 3 pixels, even when zoomed out greatly.
    Example:
       thickDrawItem on



bedFilter on
    FOR BEDS ONLY
    
    Activating this setting provides the bed filter type controls that allow you to filter
    bed items by name with wildcard matching.
    
    
    Example:
       bedFilter  on
    The bed track will be be filterable by the bed
    item names.



bedNameLabel <label>
    When a user clicks on a bed track item in the Browser image, 
    the item detail page is shown. This setting specifies an 
    alternate label for the item name on that page. Without this
    setting, the label will be "Item:".
    Example:
       bedNameLabel Gene Id



Related settings:

    baseColorUseSequence < <extFile {seqTable} <extFile> /
                        hgPcrResult / lfExtra / nameIsSequence / seq1Seq2 / ss >
    NOT FOR HUBS.  Not yet supported by bigBeds
    
    Specifies where
    item sequence can be found (if any) so that item sequence, or
    differences from genomic sequence, can be drawn when viewing a
    sufficiently small region.
    
    
    If extFile is
    specified, two additional parameters are required, the name of
    the seq table followed by the name of the extFile table to use
    in looking up the sequence. These tables are loaded by hgLoadSeq.
    
    If
    hgPcrResult is specified than a PCR result is
    used.
    If lfExtra
    is specified then the sequence of an item is found in the last
    column of the table or remote file.
    If
    nameIsSequence is specified then the 4th column (name or
    sequence) contains the sequence. (see
    hg/lib/encode/tagAlign.as)
    If seq1Seq2
    is specified then the 7th & 8th columns (seq1 and seq2)
    contain the left and right pairs of the sequence. (see
    hg/lib/encode/pairedTagAlign.as)
    If ss is specified then a
    user provided a user provided blat sequence fole is looked for.
    



baseColorUseCds <given/table <table>>
    NOT FOR HUBS.  Not yet supported by bigBeds
    Specifies where coding sequence (CDS)
    coordinates can be found (if any) so that codons can be drawn
    when viewing a sufficiently small region.  If table is
    specified, an additional parameter of a table name, in cdsSpec
    format, is required.



baseColorDefault
                    <diffBases/diffCodons/itemBases/itemCodons/genomicCodons>
    NOT FOR HUBS.  Not yet supported by bigBeds
    Specifies the default drawing mode.
    The itemBases, itemCodons, diffBases and
    diffCodons options are applicable only if the track has sequence, as
    specified by the baseColorUseSequence setting.  
    The genomicCodons, itemCodons and diffCodons are
    applicable only if the track has CDS info, as specified by the baseColorUseCds
    setting.



baseColorTickColor <lighterShade/contrastingColor>
    NOT FOR HUBS.  Not yet supported by bigBeds
    Choose a contrastingColor (this is often
    white) or lighterShade of color. This should be the
    same color as would be chosen for the base text if the user were
    zoomed in to base level.



showDiffBasesAllScales on
    NOT FOR HUBS.  Not yet supported by bigBeds
    Show base differences for all zoom levels.
    



showDiffBasesMaxZoom <basesPerPixel>
    NOT FOR HUBS.  Not yet supported by bigBeds
    Show annotations highlighting base or codon differences
    only if current zoom level does not exceed 
    basesPerPixel (a float).  showDiffBasesAllScales
    should also be set to make this useful.



showCdsAllScales on
    NOT FOR HUBS.  Not yet supported by bigBeds
    Show CDS for PSL tracks at all zoom levels.



showCdsMaxZoom <basesPerPixel>
    NOT FOR HUBS.  Not yet supported by bigBeds
    Use this setting (a float) to specify the maximum zoom-out allowed for displaying the CDS 
    for psl tracks. 
    In conjunction with this setting, showCdsAllScales must be set on and 
    showDiffBasesMaxZoom
    should be set to a value not more than showCdsMaxZoom to make this
    display configuration useful.
    
Examples:
        baseColorDefault genomicCodons
    baseColorUseCds given
    showDiffBasesMaxZoom 10000.0
    showCdsMaxZoom 10000.0
    baseColorUseCds table hgFixed.transMapGeneUcscGenes
    baseColorUseSequence lfExtra
    baseColorDefault diffCodons
    baseColorTickColor lighterShade
    showDiffBasesAllScales .
    showCdsAllScales .    
    



exonArrowsDense <off/on>
    On tracks that show
    exons or blocks within items, exon arrows allow the user to jump to
    the next exon/block outside the image.  Use this setting to
    display exon arrows even when the track is in dense mode.



itemDetailsHtmlTable <table>
    NOT FOR HUBS.  Supplemental table must be in local database.
    Use this setting to specify a table, indexed by item name, that
     contains an optional HTML fragment to display on the details page for
     this item.  The expected columns in the table are "name" and "html".
    Example:
       itemDetailsHtmlTable pseudoGeneDetails



itemImagePath <path> <suffix>

    itemBigImagePath <path> <suffix>
    
    Items can be
    associated with images and the images can be made visible with
    these two settings.  The itemImagepath specifies a
    URL path to a directory with image files named in the format 
    {name}.{suffix}.  The name is retrieved from the table or remote data
    file.  This image will be displayed on the item detaiIs page.  If
    itemBigImagePath is also supplied, then a link to a
    larger image will be provided.  If the path provided is local to
    the browser then the path should be relative.
    Example:
        itemImagePath images/myTrackImages png
    itemBigImagePath http://bigImages.com/myTrackImages jpg    
    When the user clicks
    on a item named fred, then the item details page will show
    the image images/myTrackImages/fred.png and will also
    provide a link to a larger image at
    http://bigImages.com/myTrackImages/fred.jpg.



mafTrack <trackName>
    NOT FOR HUBS
    By specifying a multiple alignments track, the item details page
    will illustrate the differences for that item across a number of species.
    
    Example:
       mafTrack multiz46way




    nextExonText <str>

    prevExonText <str>
    For tracks that
    offer multiple block items such as gene models, the next/previous
    exon arrows are usually displayed by default in the Browser.  The functionality of
    these tiny arrows is described by mouse-over "tool tips"
    that default to "Next Exon" and "Prev Exon".
    If the blocks do not represent exons, you can adjust the tool tip text to the
    appropriate information with these two settings.
    Example:
        nextExonText "Next Match"
    prevExonText "Previous Match"    



showTopScorers #
    Use this setting to
    show a list of some number of top-scoring items in a region of the genome, when
    looking at an individual item in the item details page.  The
    region will cover the current browser window coordinates.
    Currently this setting is not configurable.
    Example:
       showTopScorers 20



Examples of item base types
        type bed 3    
    The simplest bed
    format, with nothing more than a chromosome and the start and stop
    coordinates for each bed item.  There is nothing to configure.

        type bed 6 +
    colorByStrand 255,0,0 0,0,255
      ...

    type bigBed 6 +
    colorByStrand 255,0,0 0,0,255
      ...    
    The type setting for
    a bed and a bigBed are nearly identical.  Here, both type settings
    specify a track with the first 6 standard bed fields defined
    (up to strand) and with additional fields defined
    after those 6 (indicated by the '+'). The
    colorByStrand setting configures the plus strand items
    to be colored red, while the minus strand items are blue.

        type bigBed 8 .
    scoreFilter 700
    scoreFilterLimits 100:1000
    thickDrawItem on
    spectrum on
    scoreMin 700
    scoreMax 900
    color 0,0,128
    minGrayLevel   4
      ...    
    A bigBed track with
    the first 8 standard bed fields (through thickEnd),
    and no additional fields.  The '.' tells
    the Browser that the user may configure this track.  The score
    filter is explicitly declared to default to 700, and the defined
    range of 100 - 1000 suggests there are no values of interest below 100. 
    This example also colors the items blue and presents
    a spectrum or gradation of darkness based upon the score range.
    Items with a score or 700 or less are displayed as the lightest shade of
    blue, and items with a score of 900 or more are the darkest blue.  Finally, 
    the minGrayLevel ensures that the lightest shade is visible 
    to the user.  No doubt the value of '4' was chosen after experimentation 
    with the Browser display.

        type broadPeak
    pValueFilter 2.0
    pValueFilterLimits 0.0:300.0    
    This track is a
    essentially a bed 6+3 format dataset, but it has been defined with
    special features for ENCODE.  The pValueFilter applies to a field
    named pValue which is one of the 3 additional fields after the
    standard 6.



Examples of item base types
        type bigBed 6 +
    colorByStrand 255,0,0 0,0,255
      ...    
    The type setting for
    a bed and a bigBed are nearly identical.  Here, both type settings
    would define a track with the first 6 standard bed fields defined
    (up to strand) and with additional fields defined
    after those 6.  Notice that plus strand items are colored red,
    while minus strand items are blue.



        type bigBed 8 .
    scoreFilter 700
    scoreFilterLimits 100:1000
    thickDrawItem on
    spectrum on
    scoreMin 700
    scoreMax 900
    color 0,0,255
    minGrayLevel   4
      ...    
    A bigBed track with
    the first 8 standard bed fields (through thickEnd),
    and no additional fields.  The '.' is required to tell
    the Browser that the user may configure this track.  The score
    filter is explicitly declared to default to 700, and an allowable
    range for the score suggests there are no values below 100 worth
    looking at.  This example also sets the items to blue and presents
    a spectrum or gradation of darkness based upon the score range.
    Items with score 700 or less are the lightest, and items with
    score 900 or more are the darkest blue.  Finally the lightest
    shade set to be not too light with the poorly named minGrayLevel
    setting.  No doubt 4 was chosen after experimentation to see how
    it actually looks in the Browser.







wig, bigWig, and bedGraph: Signal graphing tracks 
    Another set of common track types is one that graphs a density signal along
    the genome. The graph can be a continuously varying density plot or
    one that displays a density signal in only certain regions.  The
    oldest and simplest of these is of wig format. This type has been
    improved as a bedGraph and then greatly enhanced as a bigWig.
    While there are differences among the formats, all support the basic
    graph configuration controls.  For detailed specifications of each
    type and how to prepare them for display in the Genome Browser please
    see the FAQ.



bigWig:  Signal graphing tracks 
    Another set of common track types are those that graph a density signal along
    the genome. The graph can be a continuously varying density plot or
    one that displays a density signal in only certain regions.  For data hubs
    the most common signal track type is bigWig.
    For detailed specifications of the bigWig remote data
    file format and how to prepare it for display in the Genome Browser please
    see: 
    http://genome.ucsc.edu/goldenPath/help/bigWig.html.




    type wig <low#> <high#>

    type bigWig <#> <#>
    MySQL tables of type
    wig and remote data files of type bigWig
    must declare the expected signal range for
    the data.
    Examples can be found below.




    type bigWig <#> <#>
    The remote data files of type bigWig
    must declare the expected signal range for
    the data.
    Examples can be found below.




    type bedGraph <field>

    minLimit <#>

    maxLimit<#>
    The bedGraph type
    track has the same file format as a bed file, but is loaded into
    the MySQL database in a form that can be graphed.  By default the
    value to be graphed is the fifth standard bed field,
    score;  however, you can specify a different field to use.
    Typically only the first 3 standard bed fields are included
    (chrom, start, stop) and the fourth field
    contains the signal value.  The bedGraph track offers
    a couple of important improvements over the wig track.  In wig
    tracks, the value of the signal is truncated into a single byte,
    which is effective for graphing but fails at data storage.  Also
    the wig type was originally designed for fixed-size windowing, though
    variations were added.  The bedGraph type allows for variable
    windowing and defining values even down to the base level.  To be
    clear, bigWig tracks are as versatile as bedGraphs.  It is
    only the wig format that suffers from these limitations.

    On the other hand the storage density of wig, particularly the fixed step
    variant, is vastly denser than bedGraph. In cases where the data is solely
    meant for display, the 256 levels supported by wig more than suffice.  For
    single-base or even 10-base level resolutions, bedGraph is generally not practical
    genome-wide.  Note also that wigs converted to bigWigs do not suffer the reduced
    precision of wigs loaded directly into the database.   A bigWig based on fixedStep
    wigs is the best way to represent dense graphs over the genome.

    Note that the lower and upper limits of the bedGraph signal are not declared in the type, 
    but rather are declared with 2 separate settings, minLimit and
    maxLimit.
    
    
    Examples can be found below.



alwaysZero  <off/on>
    When autoScale is set to "on" in the signal track, 
    additionally setting alwaysZero to "on" will ensure that the y=0
    value will be in view at all times. Default: off.
    



autoScale <off/on>
    The graph of the
    data displayed in the Browser image is usually scaled on the y
    axis in absolute coordinates.  However, you can display the data
    in autoScale which will ensure that the high score in the current
    viewing window will peak at the top of the graph.  Like most graph settings, 
    this is configurable by the user.  Setting it to "on" in trackDb will default 
    the track to autoScale. Default: off.
    NOTE: this option
    should be avoided if it will lead to display regions in which a low signal
    erroneously appears as significant because there is no high signal in the
    view window.
    Example:
       autoScale on



graphTypeDefault points
    The signal can be
    graphed as either "points" displayed at the signal
    value, or the default space-filling "bars".
    Example:
       graphTypeDefault points



maxHeightPixels <max:default:min>
    The amount of
    vertical viewing space for your signal track should be declared,
    though it is configurable by the user.  Typically it is set to no
    more than 100 pixels and no less than 8, with a default of 16 or
    32 pixels.
    Example:
       maxHeightPixels 100:16:8
    The browser will display the track as 16 pixels high, but the user
    can scale it up to 100 pixels.



maxWindowToQuery <integer>
    For bigWigs only
    When signal data is clicked in the Browser image, the details of the signal
    in the current viewing window are displayed.  For bigWigs that
    reference remote data, the query can be a very expensive operation if the current window 
    is large.  To avoid overburdening the Browser, the size of the window to
    query should be limited.  The value of this setting is the maximum window size in bases that
    should be queried to give the detailed signal numbers.



spanList <s1>[,s2…]
    NOT FOR HUBS.  For wig tracks only.

    Sets the data point span to just be the first span in table or list of spans in
    the loaded table you can find the spans by doing:
    "select span from <table> group by span".
    Typically spanList is only one as the example shows. Rarely there may be
    more: 
"spanList 1,1000".
    Special efforts must be made to load extra
    spans into the table for special purposes.
    Example:
       spanList 1



smoothingWindow <off/1-16>
    Often signal
    information is chunky, because a single value is given for a number of
    bases.  The graph can smooth the chunky data, presenting a display
    more reflective of the actual biology it is meant to illustrate.
    The numerical value of this setting determines how much
    surrounding data to use for smoothing: the larger the number, the
    less abrupt the curves will be.  The setting is user-configurable. Default: off.
    Example:
       smoothingWindow 4



transformFunc <NONE/LOG>
    The track's signal
    can be presented in log scale with this user-configurable setting. Default: NONE.
    Example:
       transformFunc LOG




    viewLimits <lower:upper>

    viewLimitsMax <lower:upper>
    The data of most interest in a graph
    track may be contained within a narrow range.  Typically 
    high outlier values can skew a graph and very low values may
    represent uninteresting data.  Use viewLimits to set the default
    viewing range.  Also use viewLimitsMax as suggested outer bounds.
    Example:
        viewLimits 5:20
    viewLimitsMax0:100    
    Any data points of 20 or above will be
    shown as the peak of the graph.  Data points that are below 5
    will not be displayed.  Even though the full data range extends to
    100, these settings suggest that scores of 20 or more are all
    considered highly relevant.



wigColorBy <bedTable>
    NOT FOR HUBS.  For wig tracks only.
    Regions of the
    graphed signal may be highlighted by color.  Use a bed 
    table and the color settings to shade regions of the wig
    track.
    Example:
        wigColorBy myBed
    color 175,150,128
    altColor 255,128,0    
    The bed-type table "myBed" is used to highlight
    regions of graphed signal based upon the scores in that table.
    The table may itself be a visible track, or may exist only for the
    purpose of highlighting the signal track.



windowingFunction  <mean/mean+whiskers/maximum/minimum>
    Depending upon how large of a genomic region
    is displayed in the Browser image, it may be necessary to summarize
    the actual signal.  This user-configurable setting controls how the Browser 
    collapses the signal from (for example) 100 or 100 thousand bases down to
    a single pixel.  By default
    the single pixel represents the mean of the data, though the
    maximum or minimum can alternatively be displayed.  A more informative
    option is often mean+whiskers.  This setting displays the
    mean, max and one standard deviation above mean, differentiated by shading. 
    The mean is displayed as the darkest shade, one stdDev above mean as 
    slightly lighter, and the max as the lightest shade.
    This subtle shading can quickly indicate if the
    condensed data is hiding important information that can 
    be adequately evaluated only by zooming in.
    Example:
       windowingFunction mean+whiskers
    When zoomed out, this track will show the mean
    signal but include shading representing higher scores.  The user
    may change this setting.




    yLineMark <#>

    yLineOnOff <off/on>

    gridDefault   on
    It can be useful to
    draw a line across the track's signal graph at some fixed y
    coordinate.  Do this by setting yLineOnOff to "on" and specifying the
    y coordinate with yLineMark.  These two settings are
    configurable by the user. Defaults: off and 0.0.
    Often confused with
    these configurable settings is the gridDefault, which simply draws a
    a line at y=0 across your entire track.  This setting might be
    useful if the lack of data is equivalent to a 0 signal.
    Example:
        yLineOnOff on
    yLineMark 2.5
    gridDefault on    
    The signal is graphed with a default solid line
    at zero, suggesting that any gaps in data should be interpreted as
    zero signal.  There will also be a line at the signal height of 2.5
    that may be used to emphasize which peaks in the signal reach
    this critical height.



Examples of signal graphing tracks
        type wig 0 100
    windowingFunction maximum
    viewLimits 5:20
    viewLimitsMax 0:100
    maxHeightPixels 100:16:8
    spanList 1
    wigColorBy myBed
      ...  
    This wiggle track is
    composed of a MySQL table and binary "wib" files that
    are referenced in the table.  The default windowing
    function is the maximum signal in each window (under each pixel)
    shown.  The span of bases covered by each row in
    the table is identical and can be gathered from the first row in
    the table.  The wiggle has colors supplied by the bed
    table, myBed.

        type bigWig -0.25 37.6
    windowingFunction mean+whiskers
    viewLimits 5:20
    viewLimitsMax 0:37.6
    maxHeightPixels 100:32:8
    yLineOnOff on
    yLineMark 15
    gridDefault on
    color 128,0,128
      ...  
    This bigWig format
    signal is held in a data file (which may be remote).  The more
    informative mean+whiskers windowing function is used by default in
    this track, and the signal will be 32 pixels high in the Browser
    image display.  Note that even though the signal value may be
    less than zero, that portion of the signal will not be
    displayed.  The Browser will display a line at y=0 and another at y=15, which
    may be a threshold value for this signal.  The track will be colored purple.

        bedGraph 4
    minLimit 0
    maxLimt 20
    viewLimits 5:8
    viewLimitsMax 0:20
    maxHeightPixels 100:16:8
      ...  
    This bedGraph style signal track is composed of
    a MySQL table of items, each with a score defined in the fourth
    column.  While a wiggle track is usually composed of fixed
    interval windows of signal (e.g. 200 bp), the bedGraph table may
    define a signal in varying granularities of windows with or
    without gaps.
    



Example of signal graphing tracks
        type bigWig -0.25 37.6
    windowingFunction mean+whiskers
    viewLimits 5:20
    viewLimitsMax 0:37.6
    maxHeightPixels 100:32:8
    yLineOnOff on
    yLineMark 15
    gridDefault on
    color 128,0,128
      ...  
    This bigWig format
    signal is held in a data file (which may be remote).  The more
    informative mean+whiskers windowing function is used by default in
    this track, and the signal will be 32 pixels high in the Browser
    image display.  Notice that even though the signal value may be
    less than zero, that portion of the signal will not be
    displayed.  The Browser will display a line at y=0 and another at y=15, which
    may be a threshold value for this signal.  The track will be colored purple.







genePred: Gene models and predictions
    NOT FOR HUBS.  (None of the settings in this section apply to hubs.)
    genePred is a variation of item-based tracks 
    designed especially for displaying gene
    models.  Gene models can be represented in bed 12 or bigBed 12
    type tracks, but the genePred table format allows for more detail,
    such as distinguishing between transcript, coding region, and coding
    vs. non-coding exons.  Please refer to the
    FAQ
    for information on how to prepare genePred tables for inclusion in
    the Genome Browser.



type genePred [pepTable [mrnaTable]]
    This type of track, based on MySQL tables, is for gene models and predictions.
    
    
    pepTable - Optional protein sequence table
    mrnaTable - Optional representative mRNA table
    
    Note that missing
    options can be filled with a '.' dot. Additional settings
    described below allow the grouping of gene models into classes and
    the coloring and filtering of the models by class.
    Examples can be found below.



Related settings:

    geneClasses <cl1 cl2...>
    Genes can be grouped into classes for the
    purposes of coloring and filtering.  The trick is how to
    associate each named gene with its class. Use geneClasses to create a
    list of all gene class names delimited by white space.



gClass_<xxx> <red,green,blue>
    Declare an RGB color for a named class.



itemClassTbl <table>
    Declare a MySQL table that will link classes
    to named gene models.



itemClassNameColumn <col>
    Optionally declare the column of the
    itemClassTbl that will hold the genePred names. Default: 
    name.



itemClassClassColumn <col>
    Optionally declare the column of the
    itemClassTbl that will hold the class.  Default: class.
    
Example:
        geneClasses rRNA tRNA snRNA
    gClass_rRNA 255,0,0
    gClass_tRNA 0,255,0
    gClass_snRNA 0,0,255
    itemClassTbl rnaTypes
    itemClassNameColumn rnaName
    itemClassClassColumn rnaType    
    In this genePred type track, RNA gene models
    are divided into 3 classes that are colored red, green or blue.
    The association of named gene models in the genePred table
    with the three classes is defined in the "rnaType" table.
    That table holds the RNA type in the "rnaType" column and the
    gene name in the "rnaName" column.



filterBy <field1:title=[+]option1a...>
                                [field2:title=[+]opt2a...]
    Filtering gene models by table column or even
    itemClassTbl column can be achieved by this setting. Complete
    description of this setting can be found in the 
    bed/bigBed item-based track settings. Here is an example for
    referencing the class as found in the table defined by itemClassTbl.  Not all
    track types will support externally referenced tables using filterBy
    as genePred type does.  But if you understand the CGI code that
    performs the table select, then filterBy can provide a powerful extension to
    the SQL selection used.
    Example:
        geneClasses rRNA tRNA snRNA
    gClass_rRNA 255,0,0
    gClass_tRNA 0,255,0
    gClass_snRNA 0,0,255
    itemClassTbl rnaTypes
    itemClassClassColumn rnaType
    filterBy rnaTypes.rnaType:Class=\
             rRNA|Ribosomal_RNA{color:#FF0000},\
             tRNA|Transfer_RNA{color:#00FF00},\
             snRNA|Small_Nuclear_RNA{color:#0000FF}    
    When gene models are
    selected from the genePred table for display in the Browser,
    their class is also selected from the "rnaTypes" table.  Using the
    filterBy setting creates a user selectable drop-down list box of
    3 choices or "all".  When the user filters by tRNA and snRNA (the
    green and blue choices), the mySQL select statement used by the
    Browser will be limited by the where clause "where
    rnaTypes.rnaType in ('tRNA','snRNA')".
    



autoTranslate 0
    By default, a
    predicted protein translation is generated for a gene model when
    a user views it on the details page.  This feature may be blocked 
    by setting autoTranslate to zero.
    Example:
       autoTranslate 0
     The genPred track
    will NOT show auto-generated protein sequence, perhaps because
    this track is for RNA genes.



intronGap <#bases>
    In drawing gene models, it can be useful to see
    "exon arrows" when the transcript extends beyond the current
    window.  This setting, which defaults to zero, ensures that these
    arrows will not be drawn if the interceding intron gap is less
    than the stated number of bases.
    Example:
       intronGap 12
    Don't draw exon arrows when the gap between
    exons is 12 bases or less.



defaultLinkedTables <table1>[,table2...]
    In hgTables, when selecting output fields,
    display these all.joiner-linked tables by default.
    Example:
       defaultLinkedTables kgXref



idXref <idColumn> <altIdColumn>
    By using this setting you can link alternative
    names to the gene models found in a genePred.   This is used by
    the Table Browser to establish links to other tables.
    Example:
        track knownGenes
    idXref kgAlias kgID alias    
    The ID in the name column of the knownGenes
    table is related to the alias found in the kgAlias table.



oldToNew <tableName>
    In successive versions of gene models, it can
    be helpful to map older genes to their newer models.  This can be
    done by providing a MySQL table that maps the change, and then using
    this setting to ensure the gene details page shows any changes.
    Example:
        track knownGeneOld5
    oldToNew kg5ToKg6    
    The older version of UCSC Genes references
    changes that are seen in the newer version.



Examples of genePred tracks
        type genePred
    oldToNew kg5ToKg6
    baseColorUseCds given
    baseColorDefault genomicCodons
    geneClasses coding nonCoding pseudo
    itemClassTbl myClasses
    gClass_coding 12,12,120
    gClass_nonCoding 0,153,0
    gClass_pseudo 255,51,255
    filterBy myClasses.transcriptClass:Class=\
            coding{color:#0C0C78},\
            nonCoding{color:#009900},\
            pseudo{color:#FF33FF}
      ...    
    Gene model track
    with defined classes and the option to filter by the color-coded
    classes.  Note the base level coloring option.
        type genePred . mrna
    url http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=hg17&l=$$
    urlLabel AceView Gene Summary:    
    This gene prediction
    track has associated representative mRNAs found in the "mrna"
    table. There is also an "AceView Gene Summary" url
    presented on the details page.





bam: Compressed Sequence Alignment/Map tracks
    The bam format is an
    indexed compressed data format for sequence alignments.  It is ideal
    for remote access of high-throughput sequence tags and is a native
    output format for some high-throughput sequencing (HTS) aligners.
    The format of bam data is data-file pairs, with an index in a separate file.
    These are frequently remote datasets, not residing on the UCSC server.  Please refer to
    the BAM track format page
    and the SAMtools website
    for information on how to create and deploy these remote data files
    for inclusion in the Genome Browser.



type bam
    Declares configuration settings for a track of type bam. If the bigDataUrl 
    setting is included, that data at the location specified by that URL will be
    displayed. Otherwise, a database table with a single column fileName
    can specify the location of a local file or a URL.
    If the database table includes a column seqName, a different
    BAM file or URL can be specified for each assembly sequence.
    Example can be found below.



Related settings:

    bamColorMode <strand/gray/tag/off>
    There are numerous ways to color bam tracks
    to highlight certain aspects of the data.  All of these are
    user-configurable.
    Possible settings:
    
    strand: (Default) When colored by strand, mismatched bases are highlighted in
    bright red, alignments on the reverse strand are
    colored dark red, and alignments on the forward strand are
    colored dark blue.
    gray: When colored in grayscale, items are shaded according to the 
    method specified by bamGrayMode: alignment quality, base qualities, or unpaired
    ends.
    tag: Colors are specified in "user-defined tags". SAM/BAM may
    include user-defined tags, the names of which begin with X, Y or Z and include one other letter
    or number. The user-defined tag named here specifies red, green and blue (RGB) intensities
    as a zero-terminated string (tag type Z) containing comma-separated triples of numbers
    from 0-255. For example, if a SAM/BAM record includes the tag YC:Z:255,0,0, then the
    item is colored red; YC:Z:0,0,255 makes the item blue. By default, the tag is "YC" unless
    changed using the bamColorTag setting.

    off: No additional coloring.
    




    bamGrayMode <aliQual/baseQual/unpaired>

    aliQualRange <min:max>

    baseQualRange <min:max>
    When bamColorMode is set to "gray", you
    can highlight one of the following:
    
    aliQual: (Default) The "alignment qualities" of the items are
    shaded on a scale of 0 (lightest) to 99 (darkest). Use aliQualRange
    to specify a default range.
    baseQual: "Base qualities" are shaded on a
    scale of 0 (lightest) to 40 (darkest). Use baseQualRange
    to specify a default range.
    unpaired: When "unpaired ends" is selected, an item that
    was paired in sequencing but whose mate was not mapped is colored gray,
    while singletons and properly paired items are colored black.
    
    Refer to the 
    SAM format details 
    for a discussion of these values.



bamColorTag <XX>
    You can also use RGB data associated with
    individual tags within the bam file itself.  Refer to the 
    SAM documentation 
    to understand how the RGB values are included.
    When the bamColorMode is set to "tag", the standard "YC" tag
    is used as the default. The default may be overridden with this setting.
    



noColorTag .
    The bam coloring options are all user-configurable within the browser. If your
    bam dataset contains no color tags, this setting should be included to block the
    Browser from offering the option to color tags by an embedded RGB value.
    
Examples:
        bamColorMode strand
    noColorTag    
    Sets the bam to use the default coloring scheme based on strand alignment. At the same time,
    the bam track will not offer the option to color the tags by
    RGB values, perhaps because this bam has no RGB values.
        bamColorMode gray
    bamGrayMode aliQual
    aliQualRange 20:80    
    These settings
    will highlight tags by alignment quality score.  If the score
    is at 80 or above, the tag is shaded black; if it is less than
    20, the tag is shaded very light gray.
        bamColorMode tag
    bamColorTag YC    
    The bam file includes RGB values in the YC
    field that will be used to color tags.



bamSkipPrintQualScore .
    Any bam tag can be
    displayed on the details page by clicking on it in the Browser
    image.  The details include quality scores by default.  If these
    scores are not relevant for this particular bam, they may be excluded
    from the details page with this setting.
    Example:
       bamSkipPrintQualScore .




    indelDoubleInsert <off/on>

    indelQueryInsert <off/on>

    indelPolyA <off/on>
    Insertion and deletion
    differences between tag sequences and the reference genome can be
    highlighted with the use of these settings. These options may be
    set by the user.
    
     indelDoubleInsert: Use to highlight alignment gaps in both the target
    (reference) and query (tag) sequence with double (=) lines.
     indelQueryInsert: Use to highlight an insert in the query
    sequence only by drawing an orange (|)
    or purple (|) vertical line.
    Orange lines show unalignable regions in the middle of a sequence,
    and purple highlights regions at the end of the query sequence.
    indelPolyA: Use to highlight an apparently valid
    poly-a tail by drawing a vertical green line (|).
    
    Example:
        baseColorUseSequence genbank
    indelDoubleInsert on
    indelQueryInsert on
    indelPolyA on    



minAliQual <#>
    
    When the Browser image is zoomed in to the level where individual tags are visible, the 
    tags in a bam file can be filtered to show only those with a minimum alignment quality score.
    This is a user-configurable setting. Default: 0.
    Example:
    
       minAliQual 20



Related settings:

    pairEndsByName .
    Some high-throughput sequencing technologies
    result in "paired end" tags, which are two individual bam
    records joined by their name.  If this is the case with your
    dataset, include this setting.



pairSearchRange <#>
    
    Searching to join pairs of tags by name
    will be limited to a maximum distance (default: 20,000
    bases). Use a larger range to increase the likelihood that both
    reads in a pair will be found even when only one read is in
    the viewed region.  Use a smaller range to speed image rendering.
    
Example:
        pairedEndsByName .
    pairSearchRange 5000    
    The dataset includes paired end tags. The maximum search range to join tag pairs
    by name is capped at 5000.



showNames <on/off>
    When the Browser image is zoomed in to the level where individual tags are viewable,
    the query name for each tag is shown by default.  Use this setting to hide this name.
    Example:
       showNames off



Example of a bam track
        type bam
    bigDataUrl http://hgdownload/ucsc.edu/goldenPath/hg19/bambam/barneysSon.bam
    pairEndsByName on
    showNames off
    bamColorMode off
    bamGrayMode aliQual
    indelDoubleInsert on
    indelQueryInsert on
    maxWindowToDraw 10000
      ...    
    The bam data is held in the file "barneysSon.bam" which is at an 
    internet-accessible location.  In addition to the data file, an
    associated index file must reside at the same location. The index file must have the
    same name as the data file, with ".bai" appended (e.g. barneysSon.bam.bai).





psl: Sequence alignments
    NOT FOR HUBS.  (None of the settings in this section are available for hubs, 
    although it is likely that hub support will be added in the future.)
    PSL is an alignment format in which the data is typically taken from files generated
    by BLAT or psLayout.  For further information about this format
    please refer to the FAQ and
    BLAT 
    documentation.



type psl <subtype> [otherDb]
    The psl type tracks
    require the specification of a subtype: est, mrna,
    protein or xeno.  The default, which is
    represented as ".", is regular human mRNA.  When the xeno subtype
    is selected, an additional optional parameter may be set to specify the other species
    assembly.  If present, the alignments can be color-coded by
    chromosome, and the chromosome and position (in kilobases) are shown
    in the alignments label.
    Examples can be found below.



blastRef <assembly.table>
    Include a blastRef
    to an assembly and table that contains geneId and position
    retrievable by accession id.  This information will be displayed
    in the item name.

    Example:
       blastRef hg17.blastKGRef02



colorChromDefault off
    For psl tracks of
    subtype xeno, the alignments may be colored to indicated their 
    location in the other species.  This setting is turned on by default 
    when the other species is specified in the type psl
    setting.  Use this setting to turn off chromosome coloring by default,
    offering the user the choice to turn it on. 
    
    Example:
        type psl xeno loxAfr1
    otherDb loxAfr1
    colorChromDefault off    



pred <assembly.table>
    Use the pred setting
    to name an assembly and table containing protein sequence data for
    the named alignments.
    Example:
      pred hg18.blastKGPep04



pslSequence <no/all/different>
    This setting specifies some display configuration options for
    psl tracks that also have sequence loaded.  
    

    all: Display nucleotide labels on all bases.
    different: Label only base differences. 
    no:  Allow the user to select which of the other two options is preferred.
    
    
    Example:
        pslSequence different




    transMapGene <assembly.table>

    transMapInfo <table>

    transMapSrc <assembly.table>

    transMapTypeDesc <label>
    For alignment tracks generated using the TransMap cross-species alignment
    algorithm, these settings are used to connect the transMap
    detailed information with the alignments.  
    

    transMapInfo: Use to name the table in the current assembly that 
    ties an alignment with the source assembly and feature. 
    transMapSrc: Use
    to name the table in the source species assembly that contains
    the details of the feature's source location.  
    
transMapGene: Use to name the table mapping the alignment
    to gene names in the relevant species.  Note that tables that are
    common to multiple species should be put in the hgFixed
    database.   
    transMapTypeDesc: Use to
    set a label for the type of transMapping that the alignment covers.
    
    Example:
        transMapInfo transMapInfoUcscGenes
    transMapSrc hgFixed.transMapSrcUcscGenes
    transMapGene hgFixed.transMapGeneUcscGenes
    transMapTypeDesc UCSC Gene
    baseColorUseCds table hgFixed.transMapGeneUcscGenes
    baseColorUseSequence extFile hgFixed.transMapSeqUcscGenes    
    Note that several of the named tables are in
    hgFixed, which is a database containing tables that
    are shared by multiple species and assemblies.  Also notice that
    the same table that was named in transMapGene is
    also used in this example for baseColorUseCds.
    



ucscRetroInfo
    For alignments
    illustrating retrotransposition, use this setting to name a table
    with details of the source location.
    Example:
       ucscRetroInfo ucscRetroInfo1



Examples of psl alignment tracks
        track ucscRetroAli1
    type psl
    ucscRetroInfo ucscRetroInfo1
    baseColorDefault diffCodons
    baseColorUseCds table ucscRetroCds
    baseColorUseSequence extFile ucscRetroSeq1 ucscRetroExtFile1
    indelDoubleInsert on
    indelQueryInsert on
    showDiffBasesAllScales .
    showDiffBasesMaxZoom 10000.0
      ...    
    In this example of
    retroposed genes, mature mRNA has been aligned to the genome.
    Notice there is a ucscRetroInfo table that describes the
    non-transposed gene location.  Also notice the use of the
    baseColor settings for coloring the coding sequence (CDS).


        track protBlat
    color 0,100,0
    altColor 255,240,200
    type psl protein
      ...    
    In this example of
    protein sequence blat results, the color of matching sequence is
    green, while indels (in this case introns) are highlighted with
    yellow.


        track rgdEst
    spectrum on
    color 12,12,120
    type psl est
      ...    
    This expressed
    sequence tag example will have colored alignments that are graded
    by a score thanks to "spectrum on".  Though psl tracks do not have
    a score column as part of the format, a score is
    generated based upon matches and mismatches in the alignment.  The
    shading is even more subtle in that the weight given to inserts
    varies depending upon whether the alignment is to the same or a
    different species.


        track blastzTetNig1
    color 0,0,0
    altColor 50,128,50
    spectrum on
    type psl xeno tetNig1
    otherDb tetNig1
      ...    
    This psl track is for foreign species or "xeno"
    alignments, in this case the sequence reads of a species of fish
    aligned to human.





chain and netAlign: paired species alignments
    NOT FOR HUBS.  Nor are any of the settings in this section.
    While "chain" and
    "netAlign" formats are different, they often are paired to show two
    different views of the same data.
    
    Chain tracks show
    alignments of a "query" species to a "target" genome assembly.  For
    example, a chimp panTro2 can be aligned to the human hg19 genome.
    The chain format allows for gaps in both sequences simultaneously.
    When chains are viewed in the Browser, they show solid boxes for
    alignments, separated by either single or double lines.  The single
    lines appear when an insertion occurs in the target or a deletion
    occurs in the querying species.  Double lines represent gaps in both
    species that could result from a number of causes (e.g. an inversion
    in one species).  For more information on the "chain" format, please
    refer to 
    http://genome.ucsc.edu/goldenPath/help/chain.html.
    A netAlign track
    represents the best chain for each region in the target genome.  The net
    track will show the largest, highest scoring chains that span a
    region.  When these chains have gaps, they may be filled in
    with additional chains, shown at a lower level, and gaps in these
    chains may in turn be filled at an even lower level.  These levels
    help in visualizing genome rearrangements such as inversions and
    retroposed elements.    For more information on the netAlign
    format, please refer to
    
    http://genome.ucsc.edu/goldenPath/help/net.html.




    type chain <otherDb>

    otherDb <otherDb>
    Tracks of type chain show sequence alignments
    from another species to the reference genome. This type
    requires the assembly database of the other species to be named in both the
    type setting and in the "otherDb" setting.
    Example can be found below.




    type netAlign <otherDb> <otherChainTable>

    otherDb <otherDb>
    Tracks of type netAlign show the best chains of
    sequence alignments from another species to the reference genome.
    Gaps are filled in levels, where possible.  This type requires the
    assembly database of the other species to be named in both the type setting and
    in the "otherDb" setting.
    Example can be found below.



chainColor <scheme>
    By default chains are colored by the alignment
    chromosome of the query species.  This can be overridden with this
    setting.  The three options are:
    
    Chromosome - default
    Normalized Score - chains are colored by score
    Black - no coloring occurs
    
    This setting affects
    chain but not netAlign type tracks.
    Example:
       chainColor Black



chainLinearGap <loose/medium>
    The chainLinearGap setting should reflect the
    "-linearGap" parameter used in axtChain to generate
    the track.  It represents the gap scoring matrix used and will be
    either:
    
    loose - chicken/human linear gap costs
    medium  - mouse/human linear gap costs
    
    This setting is for both chain and netAlign
    type tracks.
    Example:
       chainLinearGap medium



chainMinScore <#>
    The chainMinScore setting should reflect the
    "-minScore" parameter used in axtChain to generate the
    track.  It represents the score threshold for chains to be
    included in the set.  Default is 1000.  This setting is for both
    chain and netAlign type tracks.
    Example:
       chainMinScore 5000



chainNormScoreAvailable <yes/no>
    A given chain or netAlign track may or may not
    have a populated normScore column.  If the column exists, then
    its value can be displayed in the item details page of the
    Browser by setting chainNormScoreAvailable to yes. 
    Item coloring based upon score as selected by the
    chainColor Normalized Score setting also requires
    this setting to be yes.
    Example:
        chainNormScoreAvailable yes
    chainColor Normalized Score    




    matrix <size> <#,#,#,#,…>

    matrixHeader <b1,b2,b3,b4>

    $matrix token in html.
    The method for scoring and selecting chains and
    generating netAligns relies upon a matrix of costs for base
    substitutions.  The matrix used in the generation of any given
    paired alignment can vary depending upon such things as
    evolutionary distance and the species involved.  The matrix used
    can be dynamically included in the HTML description using three
    elements:
    
    The HTML description must have the $matrix token in it.
    The matrix to be used must be defined
    with this trackDb setting.  The format of this setting is the cell
    size of the matrix which for DNA alignments is 16.  This size is
    separated by a space from the comma-delimited array of all the
    values as the matrix cells are filled in left to right and top to
    bottom.
    The matrixHeader setting should be
    used to define the order of base transitions in the matrix.
    Typically it is “A,C,G,T “.
    
    Example:
        html chainNet
    matrixHeader A,C,G,T
    matrix 16 91,-114,-31,-123,\
                 -114,100,-125,-31,\
                 -31,-125,100,-114,\
                 -123,-31,-114,91    
    Here the $matrix token found in the
    chainNet.html file will be replaced by the following matrix:
    
    
        A C G T
        A 91 -114 -31 -123
        C -114 100 -125 -31
        T -31 -125 100 -114
        G -123 -31 -114 91
    



Examples of chain and netAlign tracks
        track chainRheMac2
    type chain rheMac2
    otherDb rheMac2
    color 0,0,0
    altColor 100,50,0
    matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
    matrixHeader A,C,G,T
    chainMinScore 3000
    chainLinearGap medium
    html chainNet
      ...

    track netRheMac1
    type netAlign rheMac1 chainRheMac2
    otherDb rheMac2
    matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
    matrixHeader A,C,G,T
    chainMinScore 3000
    chainLinearGap medium
    html chainNet
      ...    
    Both the chain and netAlign tracks above are
    for alignments of the query species/assembly rheMac2
    against the target species determined by the database this trackDb
    belongs to (e.g., human/hg19).  Because the netAlign track is
    based upon the data in the chain track, it references the track in its
    type setting.  Both tracks use the same matrix, chainMinScore and
    linear gap settings.  Methods to group these two tracks into a
    single set that share settings are described later in this
    document.





wigMaf: Multiple alignments
    NOT (currently) FOR HUBS.  Nor are any of the settings in this section.
    Multiple pairwise
    alignments can be displayed with "wigMaf" type tracks.  Tracks of
    this type may actually be composed of multiple tables and data files.
    The type setting will name the one MAF format table (with an
    associated "maf" file in /gbdb).  The optional "wiggle" setting will
    name one or more wig format tables (with an associated "wib" files)
    that contain conservation signals.  Please refer to the
    FAQ
    for information on how to prepare multiple alignment format datasets.



type wigMaf <minVal> <maxVal>
    A wigMaf type track
    is composed both of MAF format alignment (loaded with hgLoadMaf).
    The track may optionally include one or more conservation signals.  The
    signals must be within the same data range defined with the min
    and max values in the type setting.
    
    Examples can be found below.



frames <table>
    A wigMaf track can
    display gene codon translation.  The reading frame may differ
    between species.  By providing the reading frames information in a
    separate table, the user can choose which frame to use when
    viewing the data.
    Example:
       frames myCodonFrames



irows off
    By default, gaps in the non-reference species are filled with the placeholder
    character:
    

    Single Line '-': No bases in the aligned species. Possibly
    due to a lineage-specific insertion between the aligned blocks in the human genome
    or a lineage-specific deletion between the aligned blocks in the aligning species.
    Double line '=': Aligning species has one or more unalignable
    bases in the gap region. Possibly due to excessive evolutionary distance between
    species or independent indels in the region between the aligned blocks in both species.
    Pale yellow coloring:
    Aligning species has Ns in the gap region.
    Reflects uncertainty in the relationship between the DNA of both species, due
    to lack of sequence in relevant portions of the aligning species.
    
    These display conventions make it easier to visualize the columns in stacked
    alignments, but they also tend to clutter the display.  The user has the option to remove
    these placeholders by unchecking the "Display chains between alignments" option.  To
    set the default of this option to off, set irows to "off".
                
    Example:
       irows off



itemFirstCharCase noChange
    This controls if 
    species names in the multiple alignment should be capitalized in
    the pairwise display.  Set "noChange" to avoid forcing
    the first letter to lower case.
    
    Example:
       itemFirstCharCase noChange



pairwiseHeight <#>
    A wigMaf display in
    the Browser image is a stacked set of pairwise alignments to the
    target genome.  Using this setting, you can change the height of
    each pairwise signal in the image.
    Example:
       pairwiseHeight 10



speciesCodonDefault <species>
    This setting, which
    is used with "frames", declares the default species
    for the codon reading frame.
    Example:
        speciesCodonDefault hg19
    frames myCodonFrames    



speciesDefaultOff <species1> [species2 ...]
    To control which of
    the stacked pairwise alignments are displayed or hidden by default, use
    speciesDefaultOff to list the species alignments that will not be
    displayed.  Each species is specified as in the MAF
    file Organism names except embedded dots and/or spaces 
    are replaced with underscores (e.g. C. elegans ->
    c_elegans).
    Example:
       speciesDefaultOff galGal2 fr1 danRer1



Related settings:

    speciesOrder <species1> [species2 …]
    Use speciesOrder to declare the order of the
    stacked alignments.  If there are many species in your track,
    it may make sense to use the speciesGroups setting instead.




    speciesGroups <sgroup1> [sgroup2  …]

    sGroup_<sgroupN> <species1> [species2 …]
    You can include a list of "clades"
    to group the species into.   This option is an alternative to
    speciesOrder, used when there are many species.  Each
    speciesGroup in the list must have its own setting
    (sGroup_<group>), followed by a list of species,
    specified as for speciesOrder.
    
Examples:
        speciesOrder panTro1 canFam1 mm5 rn3 \
                 galGal2 fr1 danRer1
    speciesGroups Mammal Vertebrate
    sGroup_Mammal mm9 rn4
    sGroup_Vertebrate galGal2 fr1 danRer1
    Choose one of these two alternatives to display species.



speciesUseFile <fileName>
    Deprecated
    Much more rarely used, this setting can
    replace speciesOrder and speciesGroups.
    Set the speciesUseFile to a path relative to the apache cgi-bin.
    The file should contain a single species name as the first word of each line.
    Example:
        speciesUseFile speciesLists/conserved8Way.txt



summary <tableName>
    This setting contains table name of MAF summary table. The summary
    view is used when the browser display is zoomed out to contain a million
    or more basepairs.  A summary table is created from a multiple alignment MAF
    file using the utility hgLoadMafSummary.
    Example:
       summary hg17Maf8waySummary



treeImage <imageFile>
    The phylogenetic tree
    can used to show the relations of the species in the multiple
    alignment should be included as an image file.  This path is
    relative to the htdocs images directory (usually /images).
    Example:
       treeImage phylo/hg17Maf8way.jpg



wiggle <table1> <leftLabel1> <uiLabel1>
                                        [table2 leftLabel2  uiLabelN ...]
    Optionally more than
    one conservation signal can be included with your MAF display by
    using this setting.  When you include conservation wiggles, you
    can also include the standard settings for controlling signal type
    tracks.  The setting includes three parts, then (optionally)
    additional sets of three, all delimited by white space.  The first
    table is the default. The leftLabel is used to
    prefix the label "Cons" in the left label area of the Browser
    image.  The uiLabel is displayed in the track
    configuration page.  If only one table is listed, and no label is
    present, the default label "Conservation" will be
    displayed.  The labels cannot contain spaces, but underscores (_)
    will be translated to spaces in the display.
    Note: directly
    pairing the conservation signals within the wigMaf track is an
    older way of doing things.  It is easier to give users control of
    what they want to see, by including your wigMaf track and separate
    signal type tracks as subtracks within a composite track.  See the
    composite track description below.
    Example:
        wiggle phastCons8wayMammal Mammal Placental_Mammal \
           phastCons8way Vertebrate Vertebrate    



Examples of wigMaf tracks
        track hg17Maf8way
    type wigMaf 0.0 1.0
    summary hg17Maf8waySummary
    wiggle phastCons
    treeImage phylo/hg17Maf8way.jpg
    speciesOrder panTro1 canFam1 mm5 rn3 galGal2 fr1 danRer1
    speciesDefaultOff galGal2 fr1 danRer1
    irows off
    pairwiseHeight 10
    maxHeightPixels 100:16:8
    viewLimits 0.5:0.9
    viewLimitsMax 0.0:1.0
      ...    
    This 8-way
    multi-alignment for the hg17 human assembly is defined to include
    a summary table, tree image and one wiggle table containing the
    conservation score for the 8 species.  Notice that the pairwise alignments 
    for the last three species are turned off by default, and each
    pairwise alignment will have a height of 10 pixels.  With few
    species displayed by default, irows defaults to "off" as
    well, which will result in a cleaner display. Since there is a
    conservation wiggle, there are additional settings for that
    signal.
    


        track multiz46way
    type wigMaf 0.0 1.0
    summary multiz46waySummary
    frames multiz46wayFrames
    speciesCodonDefault hg19
    itemFirstCharCase noChange
    treeImage phylo/hg19_46way.gif
    speciesGroups Primate Placental_Mammal Vertebrate
    sGroup_Primate panTro2 gorGor1 ponAbe2 rheMac2 papHam1 calJac1 tarSyr1 micMur1 otoGar1
    sGroup_Placental_Mammal tupBel1 mm9 rn4 …
    sGroup_Vertebrate macEug1 monDom5 ornAna1 …
    speciesDefaultOff panTro2 gorGor1 ponAbe2 papHam1 …
    pairwiseHeight 10
      ...    
    For this wigMaf
    track, there is no wiggle defined.  In this actual
    example taken from the hg19 Genome Browser, the several conservation signals 
    displayed in concert with this multiple alignment are separate
    signal-type tracks defined as part of the "Conservation"
    composite track (see discussion of composites below).  Notice
    that the 46 species in this alignment are organized into clades
    using the "speciesGroups" setting.  Each clade has its
    own "sGroup" setting to declare the order within (not
    all species shown).





expRatio: Microarray expression data
    NOT FOR HUBS.  Nor are any of the settings in this section.
    Though
    many microarray experiments have been superseded by high-throughput
    sequencing (e.g., ChIP-seq) experiments, several microarray tracks
    still exist.  Further, microarray experiments can be the economical
    or practical choice in many instances. The datasets for the built-in
    microarray tracks in the Genome Browser are stored in bed 12+3 (bed
    15) format that includes three additional fields: expCount, expIds,
    and expScores. To display correctly in the Genome Browser,
    microarray tracks require the setting of several attributes in the
    trackDb file associated with the track's genome assembly. Each
    microarray track set must also have an associated
    microarrayGroups.ra configuration file that contains additional
    information about the data in each of the arrays. Please refer to the
    microarray track 
    section of the UCSC genomewiki
    for information on how to prepare microarray tracks.  In particular,
    that document describes the format of the groupings.ra file that
    must be associated with an expRatio track.
    Note: The expRatio data formats are reused for the
    factorSource type.



type expRatio
    Microarray data is
    displayed in the Browser by expRatio type tracks.
    The type requires additional settings:  expScale, expStep  and
    groupings.
    Example can be found below.



expDrawExons on
    If microarray data
    includes gene model or blocks within items, then the data can
    be viewed as exons and introns by setting expDrawExons
    to on.  The setting is configurable by the user.
    Example:
       expDrawExons on



expScale <#>
    Maximum expression
    value.
    Example:
       expScale 3.0



expStep <#>
    Amount to step in
    visible expression scale.  A round number close to expScale divided
    by 8 is best.
    Example:
        expScale 3.0
    expStep 0.5    



expTable <tableName>
    This setting specifies
    the name of a table in the common hgFixed
    database that contains names of experiments, etc.
    



groupings <fileName>
    A microarray dataset
    must refer to a specific set of configurations to load from the
    microArrayGroups.ra file.  Please refer to the
    microarray track 
    section of the UCSC genomewiki
    for detailed instructions on the location of this file and its
    format.  Use the "groupings" setting to point to a stanza keyed on
    "name" in that file.
    Example:
       groupings gnfHumanAtlas2Groups



Example of an expRatio track
        track sestanBrainAtlas
    type expRatio
    expScale 3.0
    expStep 0.5
    expTable sestanBrainAtlasExps
    groupings sestanBrainAtlasGroups
      ...    
    This microarray dataset refers to groupings
    defined in the "gnfHumanAtlas2Groups" stanza of the
    makeDb/hgCgiData/Human/microarrayGroups.ra  file.
    





snpNNN: specialized subclass of BED 6 for dbSNP variants
    NOT FOR HUBS.  Nor are any of the settings in this section.
    This particular variant of bed 6, identified by table name,
    is for UCSC's subset of
    dbSNP,
    NCBI's database of short genetic variants.



type bed 6 + # Track name starts with "snp"
    followed by the 3-digit dbSNP build number 
    UCSC's subset of dbSNP could be described as "bed 6 + 19"
    and is produced by a complex process starting with downloading
    several database dump files and fasta files from dbSNP, and ending
    with the creation of snpNNN and several auxiliary data
    tables. This type is not supported as a custom track type.



chimpDb <db>
    If chimp chains/nets were used to identify the chimp reference
    assembly allele at the location homologous to the human SNP, this
    specifies which chimp genome assembly was used, e.g. panTro2.



chimpMacaqueOrthoTable <table>
    If chains/nets from chimp and rhesus macaque were use to identify
    the chimp or macaque reference assembly allele at the location
    homologous to the human SNP, this specifies the database table
    that contains the mapped alleles.



chimpOrangMacOrthoTable <table>
    If chains/nets from chimp, orangutan and rhesus macaque were use to identify
    the chimp/orangutan/macaque reference assembly allele at the location
    homologous to the human SNP, this specifies the database table
    that contains the mapped alleles.



codingAnnoLabel_<table> <text>
    Deprecated; will probably be removed.
    This specifies a text label for display of <table>'s
    predictions of a SNP's effect on a protein-coding gene.



codingAnnotations <table>[,table]
    Deprecated; will probably be removed.
    This specifies one or more tables containing predictions of SNP
    effects on protein-coding genes.



defaultGeneTracks <genesTrack>[,genesTrack]
    The details page of a SNP can display the predicted functional
    affect on a gene from any genePred track.
    Since there are often many gene tracks and models, the prediction
    will depend upon the gene model used.  The user has a chance to
    choose from those available, but this setting establishes
    a default gene track or tracks to base predictions on.
    Example:
       defaultGeneTracks knownGenes



defaultMaxWeight <1|2|3>
    dbSNP assigns a weight of 1, 2 or 3 to each variant, depending
    on how many distinct mappings a variant's flanking sequences have
    to the genome.
    If this is set to 1, only uniquely mapped variants will
    be displayed by default.  If 2, only uniquely mapped
    variants and variants with a small number of duplicate mappings will
    be displayed.  If 3, all variants will be shown regardless
    of weight.  Note: some tables such as snpNNNCommon and
    snpNNNFlagged contain only uniquely mapped variants, so this
    setting has no effect on those tables.



hapmapPhase <II|III>
    The SNP details page looks for the SNP's ID in HapMap track tables
    that have different names and contents depending on whether they
    were loaded from HapMap phase II or HapMap phase III data.
    (This setting is also used by HapMap SNPs tracks.)



macaqueDb <db>
    If macaque chains/nets were used to identify the macaque reference
    assembly allele at the location homologous to the human SNP, this
    specifies which macaque genome assembly was used, e.g. rheMac2.



orangDb <db>
    If orangutan chains/nets were used to identify the orangutan reference
    assembly allele at the location homologous to the human SNP, this
    specifies which orangutan genome assembly was used, e.g. ponAbe2.



snpExceptions <table>
    This specifies an auxiliary table that contains annotations of unusual
    properties of variants.  This setting applies only to versions prior to dbSNP 
    build 132; starting with build 132, exceptions are incorporated into the 
    main snpNNN table and an auxiliary table is no longer needed.



snpExceptionDesc <table>
    This specifies an auxiliary table that maps exception keywords
    to one-sentence descriptions.



snpSeq <table>
    This specifies an auxiliary table that maps variant IDs to
    file offsets at which flanking sequences are stored.



snpSeqFile <path>
    This specifies an auxiliary file that contains the flanking
    sequences of each variant's representative submitted SNP.



Example of a SNP track
        track snp135Common
    shortLabel Common SNPs(135)
    longLabel Simple Nucleotide Polymorphisms (dbSNP 135) Found in >= 1% of Samples
    group varRep
    priority 99.0911
    visibility dense
    url http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=$$
    urlLabel dbSNP: 
    snpSeq snp135Seq
    snpExceptionDesc snp135ExceptionDesc
    defaultGeneTracks knownGene
    maxWindowToDraw 10000000
    type bed 6 +
    
    This track displays variants from dbSNP build 135 with Minor Allele Frequency (MAF)
    of at least 1%.  Flanking sequence file offsets come from the snp135Seq table,
    descriptions of unusual properties are taken from the snp135ExceptionDesc table,
    and effects of variants on protein-coding genes are shown with respect to the table
    knownGene (UCSC Genes track) by default. If the viewed region is more than
    10,000,000 base pairs, the data will not be loaded and drawn.





vcfTabix: Variant Call Format indexed by tabix
    Variant Call Format (VCF)
    is a flexible and extendable line-oriented text format developed by the
    1000
    Genomes Project for releases of single nucleotide
    variants, indels, copy number variants and structural variants
    discovered by the project. The format has been subsequently adopted by other large
    projects. When a VCF file is compressed and indexed
    using tabix
    and then made web-accessible, the Browser will fetch only the portions of
    the file necessary to display items in the viewed region. In other
    words, this is a remote data file format, as are the BAM, bigBed and bigWig formats.
    Please refer to the
    VCF and tabix track format page
    for a complete description of how to prepare and display VCF data.




type vcfTabix
    If the bigDataUrl setting is included, the data at the location
    specified by that URL will be
    displayed. Otherwise, a database table with a single column fileName
    can specify the location of a local file or a URL.
    If the database table includes a column seqName, a different
    VCF file or URL can be specified for each assembly sequence.
    Example can be found below.



Example of a VCF track
        track myVcf
    type vcfTabix
    bigDataUrl http://myorg.edu/mylab/myVcf.gz
    maxWindowToDraw 3000000
      ...    
    The data for this VCF track is stored in the remote file,
    "myVcf.gz".  That file is paired with a tabix-generated index file named
    "myVcf.gz.tbi" found in the same remote location.
    





pgSnp: Personal Genome SNP format
    NOT FOR HUBS.  (None of the settings in this section apply to hubs.)
    This format is used to
    display SNPs from personal genomes. It is used for
    the Genome Variants and Population Variants tracks.  Please refer to
    the FAQ
    for information on how to prepare personal genome SNP datasets.



type pgSnp
    Personal Genome SNP
    type tracks are essentially in "bed 4 + 3" format.
    The fourth column, name, is filled with one or more variants
    (including insertions and deletions) delimited with a '/'
    character.  The fifth column contains the number of variants found
    in the name column, while the sixth and seventh columns contain
    comma-delimited arrays of frequencies and scores respectively.
    Files in this format can be loaded into MySQL with hgLoadBed using
    the "pgSnp.sql" schema.
    
    The browser image
    displays variants as stacked boxes that show the frequency for
    each variant, if that information is in the table. The details page for each variant item
    computes any amino acid change if the variant is
    in a coding region.



pgPolyphenPredTab <table>
    Not supported for custom tracks
    Auxiliary table with likelihoods of variant damage to proteins from polyPhen.



pgSiftPredTab <table>
    Not supported for custom tracks
    Auxiliary table with likelihood of variant damage to proteins from SIFT.



Example of a Personal Genome SNP track
        track mySnps
    type pgSnp
      ...    
    A personal genome SNPs track displaying single
    nucleotide polymorphisms from the reference genome.
    





altGraphX: Alternate splicing gene model tracks
    NOT FOR HUBS.
    Gene models with
    alternate splicing can be displayed in the Browser with this type of
    track.  It supports no trackDb settings beyond the common ones.
    



type altGraphX
    Alternate slicing gene models specialized track
    used to show genome coverage.
    



Example of an altGraphX track
        track sibTxGraph
    shortLabel SIB Alt-Splicing
    type altGraphX
    url http://ccg.vital-it.ch/cgi-bin/tromer/tromergraph2draw.pl?species=H.+sapiens&tromer=$$
    urlLabel SIB link:
    idInUrlSql select name from sibTxGraph where id=%s
      ...    
    The Swiss Institute of Biology's
    alternative splicing track provides an external link via the url
    setting.  But the actual "tromer" term in the value
    will be filled in with the results of a query to the sibTxGraph
    table.  With enough obscure settings, the Browser accomplishes
    subtle things.





bedDetail: Text extended bed track
    NOT FOR HUBS.
    This is an extension of
    BED format. BED detail uses the first 4 to 12 columns of BED format,
    plus 2 additional fields that are used to enhance the track details
    pages. The first additional field is an ID, which can be used in
    place of the name field for creating links from the details pages.
    The second additional field is a description of the item, which can
    be a long description and can consist of html, including tables and
    lists.



type bedDetail <#>
    Extended bed type
    format that has a text description embedded in the table for each
    item.  The format can vary between 4 and 12 standard bed columns
    plus two additional ones.  The number of columns (including the 2
    bedDetail specific columns) must follow the "bedDetail" term in
    the type setting.
    Example can be found below.



Example of a bedDetail track
        track microattrLoci
    type bedDetail 14
    itemRgb on
    url http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&sendto=t&extrafeatpresent=1&list_uids=$$
      ...    
    This bedDetail contains details for each item
    formatted for HTML display.  In addition each item has an "id" as
    distinct from the "name" and that id is used in the outside link
    url displayed in the item details page.





clonePos: Genome coverage tracks
    NOT FOR HUBS.
    This is a specialized
    format track that is only used for showing the coverage in the human
    genome.  It supports no trackDb settings beyond the common ones.



type clonePos
    A specialized track used to show genome
    coverage.
    



Example of a clonePos track
        track clonePos
    shortLabel Coverage
    longLabel Clone Coverage/Fragment Position
    type clonePos
    altColor 180,180,180
      ...    
    The Coverage track for the human genome will
    vary in color between black and light gray, based upon the cloned
    sequence coverage depth.





ctgPos: Physical map contigs tracks
    NOT FOR HUBS.
    This is a specialized
    format track that is used for "physical map contigs" on
    the human genome.  It supports no trackDb settings beyond the common
    ones.



type ctgPos
    A specialized track used to show the locations
    of contigs on the physical map.
    



Example of a ctgPos track
        track ctgPos2
    shortLabel GRC Map Contigs
    type ctgPos
    url none
      ...    
    The GCR Map Contigs track would normally
    generate a URL to NCBI, but in this case, the URL has been
    explicitly blocked.





downloadsOnly: Specialized track that contains only downloadable files
    NOT FOR HUBS.
    The ENCODE tracks all
    have a special directory and CGI support for downloading files.  This
    can be very helpful for organizing access to the often very large
    number of downloadble files associated with an ENCODE track.  There
    are a handful of datasets that don't readily lend themselves for
    visualization in our Browser but are nonetheless a necessary
    component of the ENCODE data as a whole.  Therefore, downloadsOnly
    type was developed to provide easy access to these sets of
    downloadable files.



type downloadsOnly
    A specialized track
    that provides access to a set of downloadable files, and is
    currently ENCODE only.  A downloadsOnly type track does not get
    visualized in the Browser.
    Example can be found below.



fileSortOrder ...
    The fileSortOrder setting is required for
    downloadsOnly type tracks.  A complete description can be found in
    composite tracks section of this document.  It requires each file
    to be defined as an object in the metaDb and each of those objects
    to refer to a "composite" which will be the name of this track and
    the directory name where the files are located.  The
    "fileSortOrder" defines the column and default sort order.  The
    user will be able to sort and filter the list of files.



Example of a Downloads Only track
        track wgEncodeUmassWengTfbsValid
    type downloadsOnly
    fileSortOrder cell=Cell_Line \
                dccAccession=UCSC_Accession \
                fileSize=Size \
                fileType=File_Type \
                dateSubmitted=Submitted \
                dateUnrestricted=RESTRICTED<BR>Until
    wgEncode 1
      ...    
    The Browser will not provide visualization of
    this track but will provide access to downloading any number of
    files organized into a single group.  The downloads page 
    presents those files in a table with a number of columns that are
    sortable and possibly filterable.  Much of the presentation and
    organization relies upon settings established in the metaDb for
    this track. However, the fileSortOrder setting has requested six
    specific columns to be presented in the desired order.





encodeFiveC: Five C Chromatin interaction track
    NOT FOR HUBS.
    This is a specialized
    format track that was used for displaying long distance
    chromatin/chromatin interaction evidence.  Essentially a "bed"
    type track displaying locations in the genome.  The details page of
    each location presents a list of other locations within the genome
    that may have functional interactions.



type encodeFiveC
    A specialized track that was used to show the
    locations where  chromatin may have interactions with other
    chromatin locations.
    



interTable <tableName>
    Each location found in the track's main table
    should have associated regions defined in the interactions table
    named with this setting.  The interactions table format
    is essentially a "bed 7 + 1".



interTableKind <label>
    The table of interactions is presented on each
    item's details page and is titled as "Top ___ interactions"



Example of an encodeFiveC track
        track encodeUw5cGM06990dS9013DhsLoci
    type encodeFiveC
    color 200,100,0
    interTable encodeUw5cGM06990dS9013DhsInter
    interTableKind TSS
      ...    
    This Five C interactions track will be
    displayed as colored items.  The associated chromatin regions are
    drawn from a second table.  The kind of associations are
    transcription start sites.





factorSource: Combined items tracks
    NOT FOR HUBS.
    Factor source is not a
    group track, but a track that is made from a group of sources, which
    may themselves be Browser tracks.  This is a specialized type of
    "item" based track of "bed 15" format, the same format
    used for type expRatio.  Its purpose is to
    display transcription factors as detected in multiple cell lines,
    though it might be adaptable for any type of item that piles up
    into overlapping locations and will belong to one of several
    categories.  However, this type was specifically designed for
    combining transcription factor (TF) binding evidence from multiple
    cell lines into a single track.  As a bed type track, it consists of
    items or regions where there is evidence of TF binding. To the left
    of each item, the factor name is displayed, while to the right a
    coded list of cell types where the evidence has been found is
    displayed.  Unlike most item-based tracks, a second table is required
    to describe the cell lines.  Use the program hgBedsToBedExp to create
    the tables from a collection of simpler beds, one for each
    transcription factor/cell interaction.



type factorSource
    A bed 15 based table
    format with overlapping items.  This is a specialized track type
    designed for holding transcription factor binding evidence across
    multiple cell lines.  The format is the same as used for
    microarray expression.
    Example can be found below.



sourceTable <table>
    The factorSource type tracks need a secondary
    table that holds descriptions of the sources.  This is where cell
    line abbreviations are declared and associated with actual cell
    lines.



inputTrackTable <table>
    When viewing the details for a factorSource
    track item (typically a TF binding site), additional information
    about the cell line evidence can be displayed.  This setting names
    a table that will hold the additional information.  It is used in
    conjunction with the inputTableFieldDisplay setting.



inputTableFieldDisplay <f1> [f2...]
    If there is an inputTrackTable defined with
    your track, the fields that are to be displayed should be declared
    with this associated setting.



filterBy <field1:title=[+]option1a...>
                                [field2:title=[+]opt2a...]
    This setting provides user filtering of factorSource items by factor name.
    The simplest use is to include a comma-separated list of all factor names in the track as
    an argument to the setting.
    A complete description of this setting can be found in the 
    bed/bigBed item-based track settings.



motifTable <table>
    
    A bed 6 table that holds motif regions
    to highlight within factorSource items.



motifMapTable <table>
     If motif names differ from or are not unique for factorSource item names
    in the motifTable, this table can used to remap the names.
    This table has a simple 2 column format: char(255) factor, char(255) motif.



motifPwmTable <table>
    When viewing the details of a factorSource track item containing
    a binding motif in the motifTable, the 
    consensus motif sequence and sequence logo image can be displayed. 
    This setting names the table holding the position weight matrices 
    that provide this information.



motifMaxWindow <integer>
    Display of highlighted motifs in a factorSource track can be limited using
    this setting.  In large genomic regions motifs are not well distinguished in
    the display, and performance is improved by suppressing the feature.



motifDrawDefault <on/off>
    If a factorSource track has a motifTable, this setting controls whether motifs 
    are drawn by default.  It is also configurable by the user.




Example of a factorSource track
track tfbsByCellLines
type factorSource
sourceTable myCellLines
inputTrackTable myCellLineAssociations
inputTableFieldDisplay cellType treatment lab
motifTable transfacMotif
motifPwmTable transfacMotifPwm
motifMapTable transfacMotifTarget
motifMaxWindow 30000
motifDrawDefault on
    ...
This track will show transcription factor (TF)
binding evidence found in multiple cell lines.  Each item represents
a particular TF, along with the cell lines that show
evidence of binding in that location.  The secondary sourceTable
holds the definitions of each cell line abbreviation.  A third
table is declared with inputTrackTable and carries details for
each cell line that should be seen in the Browser.  When viewed in
item detail, 3 fields (cellType, treatment and lab) will be seen
for each cell associated with the particular TF binding location.





rmsk: Repeat masking tracks
    NOT FOR HUBS.
    This is a specialized
    format track that is used only for the repeat-masking track.  For
    completeness it is being briefly described here.  These tracks are
    created created by using Arian
    Smit's RepeatMasker
    program, which screens DNA sequences for interspersed repeats and low
    complexity DNA sequences.



type rmsk
    The repeat masker
    tracks contain uniquely formattted data for the special function
    of repeat-masking.
    
    Example can be found below.



Example of a Repeat Masking track
        track rmsk
    spectrum on
    type rmsk
    maxWindowToDraw 10000000
      ...    
    The repeat masker track will have individual
    repeat items shaded by a measure of how exact a repeated element
    is withing the stretch of repetition. This track is restricted to
    display at less than 10 million base resolution.
    





snake: Self referencing alignment tracks -
    EXPERIMENTAL
    NOT FOR HUBS.
    This is a specialized
    format track that shows the snaking course of bi-directional and
    overlapping alignments.  This format can help illustrate inversion-type 
    rearrangements that align to the plus strand, then the minus strand, 
    and again to the plus strand.  It can also be used to illustrate overlapping
    alignments, such as when a duplication has occurred compared to the
    reference genome.




    type snake <db>

    otherDb <otherDb>
    A specialized track
    used to show the path of snaking alignments that represent
    chromosomal rearrangements, duplications and inversions.   Since
    this type is almost always a mapping between two species or two
    assemblies of the same species, the type must also declare that
    species/assembly by database name.
    As with chains and netAligns, which typically show mappings between two assemblies, 
    the "otherDb" setting is also needed to declare which other genome and assembly
    the data in this track represents.



Example of a snake track
        track snakeMm9
    type snake mm9
    otherDb mm9
    color 100,50,0
    altColor 255,240,200
    spectrum on
      ...    
    This snake track will illustrate chromosome
    rearrangements that have occurred on the mouse mm9 genome as seen
    when it is aligned to the human genome.
    





Predefined major track groupings
    NOT FOR HUBS.
    The simplest grouping:



group <groupId>
    All tracks belong to
    one of several groups.  Hub tracks belong to the group that
    encompasses their hub.  Other tracks belong to one of the
    predefined groups.  For hg19 the following groups are defined:
    
    map - "Mapping and Sequence"
    phenDis - "Phenotype and Disease Associations"
    genes - "Genes and Gene Prediction"
    rna - "mRNA and EST"
    expression - "Expression"
    regulation - "Regulation"
    compGeno - "Comparative Genomics"
    neandertal - "Neandertal Assembly and Analysis"
    varRep - "Variation and Repeats"
    
    If no group is set for a built-in track, then the track will end up
    in the Experimental Tracks section at the bottom.



Example of a track belonging to a predefined group
        track myTrack
    group regulation
      ...    





Supertrack settings
    The first 
    hierarchical container is called the supertrack, which may be thought of as 
    a folder that holds other tracks. The Browser currently supports only one
    level of supertrack folders.  Generally the subtracks
    of a supertrack are of differing types.  If all the children are
    of the same type, it is often better to use the "compositeTrack" grouping
    described below.  If all of the children are wig or bigWig tracks, it may
    be of interest to use a signal overlay "container multiWig" grouping. Signal
    overlay tracks display the signal data from several subtracks as colored
    transparencies, making it possible to see the data of several tracks together
    in a condensed view. See the multiWig section for more information. 
    Supertracks can contain
    composite tracks and container multiWigs, but not vice versa. With supertracks,
    composite tracks, and container multiWigs, children will inherit the settings
    from their parents, but can override their parent settings within their own stanzas.



superTrack on
    To declare a supertrack, simply add this
    setting to a track definition that will hold a few standard
    settings. To set a supertrack to display as default add the word show,
    superTrack on show, to the end of the statement.
    When attempting to debug visibility settings, it may be 
    helpful to read the note about
    inheritance found below. 
    



parent <superTrack>
    Membership in a supertrack, composite, or aggregate track is declared by the
    child, not the supertrack itself.  Any number of children may
    belong to one supertrack, but ten is a suggested maximum number for usability
    considerations.  Stylistically, children's stanzas within the trackDB typically are indented
    directly under the stanza of the parent. However, this is less frequently the case with
    supertracks, because the children are often scattered in other places within the trackDb 
    file, or the supertrack children are themselves composites containing
    additional indentation that makes enforcement of the supertrack
    indentation impractical.



Example of a Supertrack
        track myFolder
    superTrack on
    group regulation
    shortLabel My Folder
    longLabel My folder keeps my tracks together
      ...

        track myFirstTrack
        parent myFolder
        visibility dense
          ...

        track mySecondTrack
        parent myFolder
        visibility none
          ...    
    The supertrack called "My Folder"
    contains two children.  All will be grouped under 
    "regulation".  Notice that the first track is visible by
    default (if the supertrack itself is visible), but the second
    track is not.





Composite Tracks
    Composite tracks are
    another level of hierarchy and are meant to group very similar tracks
    (called "subtracks") together such that they can all
    share the same configuration settings.  In its simplest form a
    composite holds tracks all of the same type (such as bigBed).
    Initially, all track within the set are configured identically.
    Usually only some of the subtracks are visible by default, and these
    will have the same display mode (e.g., dense)
    and optional settings (e.g., viewLimits).
    While default settings cover the entire composite of related tracks,
    in most cases individual subtracks can be configured by the user
    independently of the composite settings.  However, once individual
    subtrack settings are made, they can be overridden by new choices made at
    the composite level.  It may be helpful to read the "Note about
    inheritance" found below.
    Currently only the following track types can be organized into a 
    composite: item-based tracks (bed, bigBeg, broadPeaks, etc.), signal-based
    tracks (wig, bigWig, etc.), other remote file-based tracks (bams,
    vcf, etc.), chains/nets, genePred, psl, and wigMaf-type tracks.



Composite Tracks
    Composite tracks are
    another level of hierarchy and are meant to group very similar tracks
    (called "subtracks") together such that they can all
    share the same configuration settings.  In its simplest form a
    composite holds tracks all of the same type (such as bigBed).
    Initially, all track within the set are configured identically.
    Usually only some of the subtracks are visible by default, and these
    will have the same display mode (e.g., dense)
    and optional settings (e.g., viewLimits).
    While default settings cover the entire composite of related tracks,
    in most cases individual subtracks can be configured by the user
    independently of the composite settings.  However, once individual
    subtrack settings are made, they can be overridden by new choices made at
    the composite level.  It may be helpful to read the "Note about
    inheritance" found below.



compositeTrack on
    To declare a composite, simply add this setting
    to a track definition, along with a few standard settings.
    The subtrack stanzas always follow immediately after the
    composite track delaration and are indented from it.
    Note that since children of composites inherit their parent's
    settings, many more trackDb settings will be found at the
    composite level than at the supertrack level.



parent <composite> [off/on]
    Membership in a composite is declared by the
    subtrack child, not the composite itself, through this setting. Any number of subtracks may
    belong to one composite, but display performance degrades significantly beyond a
    few hundred.  Set the parent setting to "on" to 
    indicate whether a subtrack should be visible (checked, selected) by default.  



allButtonPair on
    When a simple composite track presents a short list of
    subtracks, it can be convenient for the user to have an easy way to select or
    deselect all of them.  Include this setting to display an "All 
    "
    
    (plus and minus button pair) for the user's convenience.  If
    the list contains more than 10 subtracks, other methods may be
    more useful for organizing and selecting subtracks (described below).
    



centerLabelsDense <off/on>
    
    By default, only the composite track's single center label is shown when the 
    subtracks are displayed together in the Browser dense mode. 
    If centerLabelsDense is set to "on", the Browser will display a center 
    label for each subtrack. 
    



dragAndDrop on
    
    The subtrack list in the configuration page can be rearranged by setting
    a sortOrder, as described below, 
    or by allowing the user to drag and drop the subtracks to a new order 
    if enabled with this setting. The changed order will also be seen in the track 
    image.  However, the order of tracks can always be rearranged through 
    drag and drop, directly in the image.  Reordering subtracks in the image 
    will not be reflected in the configuration page. Note: This setting will not
    work correctly if 'container multiWig' is specified.




Example of a Composite track
        track myComposite
    compositeTrack on
    parent myFolder
    shortLabel My Composite
    type bigWig 0 1.0
    viewLimits 0.0:0.2
    allButtonPair on
    dragAndDrop on
      ...

        track myFirstSubtrack
        parent myComposite on
          ...

        track mySecondSubtrack
        parent myComposite
          ...    
    The composite with two subtracks shown.  All
    subtracks are of type bigWig and all have a default viewLimits of 0 - 0.2.  
    Notice the first subtrack is checked by default, but the second is not 
    (parent setting).  However, the Browser will display two buttons 
    (allButtonPair setting) that allow the user to
    select all subtracks, or deselect all of them and then check only those of 
    interest.  The user may reorder the subtracks by dragging them on the composite
    configuration page (dragAndDrop setting). Note: The dragAndDrop setting 
    will not work correctly if 'container multiWig' is specified.





Subgroups
    Within a composite track, two different grouping styles can be used to allow 
    the user to select tracks for display in the Browser.
    This section describes the configuration of "subgroups"; "views" are discussed in
    a subsequent section.
    
    The subgroup can be used for selecting sets of subtracks for display based on certain
    characteristics of the data. For instance, if  "cell" and "antibody" are
    defined as subgroups within a composite track, the user will be able to select
    subtracks based on specific cell types and antibodies to display in the Browser.  Up to 9
    subgroup types can be defined for a composite.  However, to minimize the complexity,
    it is strongly recommended that only two subgroups be defined
    for a given composite track. These will be presented in a simple X/Y matrix that is easy for
    the user to understand and navigate. It is possible to define more subgroups in additional 
    "abc" dimensions that will be presented to the user as drop-down multi-select dialogs,
    but use of these should be avoided or minimized.




    subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a>
                        [mTag1b=mTitle1b…]

    subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a>
                        [mTag2b= mTitle2b…]
    Up to 9 subgroups may be declared, one per line.  Each subgroup declaration
    must include a whitespace-delimited tag, title, and one or more tag/title 
    membership pairs joined by an '=' equals sign. 
    
     tag: Used in the code to select
    and sort subtracks based upon their membership.  Tag names
    must be alphanumeric, begin with a letter, and be formed such that the
    desired sort order of the member subtracks will result.
     title: Label of the subgroup as it appears on the 
    selection matrix that is displayed to the user, e.g.,"Antibody". Spaces within
    titles must be replaced by '_'.  A limited amount
    of HTML is allowed in titles, such as the insertion  of Greek letters using an HTML
    code. Any use of HTML should be tested to ensure that it displays correctly.
    
    Because subgroup settings are often lengthy, it is recommended that the 
    '\' line continuation character be used to break up the setting over
    multiple lines for easier reading. 



subGroups <gTag1=mTag1?> [gTag2= mTag2?]
    The subtracks themselves declare their
    membership in a group with the subGroups setting.
    Each subtrack must declare its membership in all of its
    composite's subgroups.  Notice that membership is declared
    by pairs of tags: the group tag (e.g. gTag1) is paired with that
    group's member tag (e.g. mTag1b) as gTag1=mTag1b (cell=K562).



dimensions <dimX=gTag#> [dimY=gTag#] [dimA=gTag# ...]
    In order to define the type of UI desired for
    selecting subtracks based upon groups, additional settings are
    needed at the composite level.  For a one- or two-dimensional array of
    checkboxes, declare the dimensions X and Y.  Additional dimensions (called
    "abc") can be declared with this setting as dimA, dimB, etc.  
    Note that the order of the subgroups in a dimension is exactly the same as 
    the order they appear in the subGroup# setting, regardless of whether
    the subtrack list is sorted by tags.



filterComposite <dim[A/B/C][=one]> [dimB dimC ...]
    For the "abc"
    dimensions, rows of checkboxes will be shown by default.  However, this
    UI can be confusing, especially combined with a one- or two-dimensional matrix.
    Instead, it is recommended that you organize "abc"
    dimensions as drop-down multi-selects, often referred to as
    "filter" boxes due to their similarity to the
    filterBy setting discussed
    above.  Declare the subtrack filter boxes with the filterComposite
    setting.  Filter composites may work with or without the X/Y
    matrix, but are restricted to the "abc" dimensions.
    By default, the filter box for selecting
    subtracks is multi-select, meaning more than one choice is
    allowed.  It is possible to restrict this to a single choice by
    adding the "=one" option to the filter box definition.
    This might make sense when there are only 2 choices.  The choice
    of "all" is always available, while choosing nothing is an invalid
    case.



    dimension<?>checked <mTag1a>
                                [mTag1b …]
    One more complication in the selection process is
    determining which subgroup options are selected by default.  In the
    case of the X/Y matrix this can be determined by what subtracks
    are currently checked.  But, "abc" dimensions must have their
    selected state declared explicitly using the
    dimension<?>checked setting.



controlledVocabulary <pathToFile> <gTag#=mdbVar>
                            [gTag#=mdbVar …]
    NOT FOR HUBS. Currently used only by ENCODE
    In ENCODE, subgroups
    are often based on metadata terms declared in the metaDb table and defined
    in the "controlled vocabulary", which is 
    stored as an ra file.  In this situation, the labels of these
    terms, as they are displayed in the track configuration page, can
    be linked to the controlled vocabulary definitions.  These links
    can be quite useful, as the term definition may include protocol
    documents and validation evidence.  In order to establish the
    links, each subGroup's tag must be tied to the actual metaDb
    term.
    
    



sortOrder <gTag#=+/-> [gTag#=- …]
    When declaring subgroups, it is often useful to
    sort the subtrack list by those subgroups.  By including a
    sortOrder setting, long sets of subtracks are more easily
    organized and navigated by the user.  If there are only a few
    subtracks in the composite, sorting may be of little value and 
    dragAndDrop may be a better option.
    Currently only subgroups can be defined in the sortOrder, but it
    is anticipated that this will expand to include short and long
    labels as well.  Sorting will occur on the tag values defined in the 
    subGroup# and subGroups settings.  By sorting
    on tags, non-alphanumeric orders can be defined.



fileSortOrder <var=val> [var=val ...]
    NOT FOR HUBS. Currently used only by ENCODE
    Some composite track sets have their own
    directories of downloadable files and a special CGI for accessing
    those files.  In order to see the CGI interface for the download
    directory, the composite needs an object for each file defined in
    the metaDb.  The trackDb stanza for the composite also needs to
    have the fileSortOrder setting defined.  The setting is defined as
    a set of variable=value pairs, which defines the default sort
    order on metaDb variables.  The "var" portion of the each pair is
    a term defined in the metaDb for all of the file objects in the
    directory.  The "var" may also be "fileType" or "fileSize",
    which are not defined in the metaDb. The "val" is the title that the
    user will see as the column header for the sortable table of
    files.  This value can contain and '_' for spaces and limited HTML
        codes and special characters.  As always, you are encouraged to
    experiment.  The '\' continuation character should be used to
    break up this long setting into readable lines.
    



Examples of Composite tracks with Subgroups
        track myComposite
    compositeTrack on
    subGroup1 cellLine Cell_Line \
            A1GM12=GM12878 \
            CD14=CD14&#43; …
    subGroup2 ab Antibody \
            H3K04ME3=H3K4me3 \
            H3K36ME3=H3K36me3 …
    dimensions dimX=ab dimY=cellLine
    sortOrder cell=+ ab=+
      ...

        track myFirstSubtrack
        parent myComposite on
        subGroups cellLine=CD14 ab=H3K04ME3
          ...    
    This examples shows a composite with
    one subtrack and two subgroups.  The
    dimensions setting declares X and Y dimensions, which will display
    a 2D matrix on the composite's configuration page.  Notice that the
    title of the cellLine subgroup contains a blank space filled in
    with '_'.  The second cell line, "CD14+", includes an HTML encoding
    for '+' in its title, The two subgroups participate in the default
    sort order of subtracks, but they each have non-standard sort orders.  In the 
    cellLine subgroup, GM12878 sorts first by starting its tag with "A".  The 
    antibodies have numbers in their titles, but the tags expand
    the number with "0" to pad the spacing.  This ensures
    H3K4me3 sorts before H3K36me3.

        track myCompositeIs3D
    compositeTrack on
    subGroup1 cellLine Cell_Line \
            A1GM12=GM12878 \
            CD14=CD14&#43; …
    subGroup2 ab Antibody \
            H3K04ME3=H3K4me3 \
            H3K36ME3=H3K36me3 …
    subGroup3 treat Treatment \
            TNFA=TNF-alpha \
            ZNONE=None …
    dimensions dimX=ab dimY=cellLine dimA=treat
    filterComposite dimA
    dimensionAchecked ZNONE
    controlledVocabulary encode/cv.ra cellLine=cell \
                                    ab=antibody \
                                    treat=treatment
    sortOrder cell=+ ab=+ treat=-
    fileSortOrder cell=Cell_Line \
                antibody=Antibody \
                fileSize=Size
      ...

        track myFirstSubtrackIn3D
        parent myCompositeIs3D on
        subGroups cellLine=CD14 ab=H3K04ME3 treat=ZNONE
          ...    
    In this second example composite,
    one subtrack and three subgroups are shown.  As in the previous example, the
    dimensions setting declares X and Y dimensions, resulting in 
    a 2D matrix of "Antibody" and "Cell Line" options.  A third "Treatment" subgroup is 
    declared as the "A"
    dimension; the user will be able to select subtracks for this
    dimension via a dropdown multi-select filter box.  All three subgroups 
    participate in the default sort order of subtracks, and the treatment subgroup is 
    sorted in reverse order by default.  The "None" treatment
    sorts before all others (in reverse order) by beginning the tag with
    a "Z".  Note that for this "A" dimension,
    the "None" treatment will be selected by default.  By
    declaring the proper settings, using subGroups to organize a
    composite can be quite powerful.

    This example illustrates that
    subgroups, dimensions, and (in the case of ENCODE) controlled vocabulary and
    metadata all must be linked together for the composite to fully
    work.  Further, the actual terms, programmatic "tags"
    and user visible titles all have different constraints and roles
    to play in establishing this cohesion.  Subgroup tags are used to
    organize subtracks, while lettered dimensions organize the
    configuration page to more easily select subgroups of subtracks.
    For ENCODE tracks, the subgroups may be represented as metadata
    "terms" (distinct from tags) that are often carefully
    defined by a controlled vocabulary.  In the example above, the tag
    "ab" is used to organize subtracks into subgroups but
    is also tied to dimension X.  This ensures that antibodies will
    appear as the horizontal dimension in the 2D matrix on the
    configuration page, and the selection of an antibody will select the
    associated subtracks.  Of course the user does not see the
    antibody as "ab" but "Antibody".  Going
    further, the term as defined in controlled vocabulary is
    "antibody", so that for all the tables and files
    associated with this composite track, their metaDb objects should
    contain an "antibody" var and a given antibody (e.g.
    H3K4me3) will be found in the controlled vocabulary with a
    validation document.  All the relationships can be confusing, but
    the trackDb settings, if done correctly, can tie all these
    elements together in a nice cohesive package.





Examples of Composite tracks with Subgroups
        track myComposite
    compositeTrack on
    subGroup1 cellLine Cell_Line \
            A1GM12=GM12878 \
            CD14=CD14&#43; …
    subGroup2 ab Antibody \
            H3K04ME3=H3K4me3 \
            H3K36ME3=H3K36me3 …
    dimensions dimX=ab dimY=cellLine
    sortOrder cell=+ ab=+
      ...

        track myFirstSubtrack
        parent myComposite on
        subGroups cellLine=CD14 ab=H3K04ME3
          ...    
    This examples shows a composite with
    one subtrack and two subgroups.  The
    dimensions setting declares X and Y dimensions, which will display
    a 2D matrix on the composite's configuration page.  Notice that the
    title of the cellLine subgroup contains a blank space filled in
    with '_'.  The second cell line, "CD14+", includes an HTML encoding
    for '+' in its title, The two subgroups participate in the default
    sort order of subtracks, but they each have non-standard sort orders.  In the 
    cellLine subgroup,  GM12878 sorts first by starting its tag with "A".  The 
    antibodies have numbers in their titles, but the tags expand
    the number with "0" to pad the spacing.  This ensures
    H3K4me3 sorts before H3K36me3.

        track myCompositeIs3D
    compositeTrack on
    subGroup1 cellLine Cell_Line \
            A1GM12=GM12878 \
            CD14=CD14&#43; …
    subGroup2 ab Antibody \
            H3K04ME3=H3K4me3 \
            H3K36ME3=H3K36me3 …
    subGroup3 treat Treatment \
            TNFA=TNF-alpha \
            ZNONE=None …
    dimensions dimX=ab dimY=cellLine dimA=treat
    filterComposite dimA
    dimensionAchecked ZNONE
    sortOrder cell=+ ab=+ treat=-
      ...

        track myFirstSubtrackIn3D
        parent myCompositeIs3D on
        subGroups cellLine=CD14 ab=H3K04ME3 treat=ZNONE
          ...    
    In this second example composite,
    one subtrack and three subgroups are shown.  As in the previous example, the
    dimensions setting declares X and Y dimensions, resulting in 
    a 2D matrix of "Antibody" and "Cell Line" options.  A third "Treatment" subgroup is 
    declared as the "A"
    dimension; the user will be able to select subtracks for this
    dimension via a dropdown multi-select filter box.  All three subgroups 
    participate in the default sort order of subtracks, and the treatment subgroup is 
    sorted in reverse order by default.  The "None" treatment
    sorts before all others (in reverse order) by beginning the tag with
    a "Z".  Note that for this "A" dimension,
    the "None" treatment will be selected by default.  By
    declaring the proper settings, using subGroups to organize a
    composite can be quite powerful.





Views
    In addition to subgroups, a single
    composite can be divided into multiple "views".  Recall
    that a composite should be made up of subtracks of the same type.
    However, different types of subtracks can be combined into the same
    composite track if they are in separate  "views".  While
    views are like subgroups in many ways, they can carry their own
    settings.  This is necessary because the views within a composite may be for different
    types that have their own distinct configuration settings, for example bigBeds and
    bigWigs. 
    The "view" (or
    "multi-view") organization is typically used when the
    same basic data is stored in multiple formats and granularities.  For
    example, a collection of views may include short read sequence alignments (type bam), signals
    representing pile-ups of aligned reads (type bigWig), and the  peaks (type
    bigBed) that are called in regions where  the evidence of experimental result is
    deemed significant.  These three "views" of the same
    experimental data can be seen more informatively as a cohesive set
    within a multi-view composite track.
    Views are declared both
    as a subgroup and as a separate track stanza.  A composite with
    multiple views has only views as children, and each view will have one
    or more subtracks as children.  The three levels must be defined
    together with indenting to make the hierarchy obvious.
    
    
A note about
    inheritance. Subtracks
    will inherit settings from their parents (both from composites and
    from views).  This is true when the setting is inheritable, which is generally
    the case.  Obvious exceptions are settings that are
    relevant only to the higher level.  Inheritance follows the "closest
    to home" paradigm in which a setting at the subtrack level
    takes precedence, followed by the view level setting, and finally 
    the composite level setting.  This inheritance applies to both the trackDb default settings 
    and the choices made by a user. Settings made 
    by the user involve a timing element as well:  a change to 
    a parent-level setting will override all settings of
    the same type for its children.  If the user subsequently makes a subtrack
    setting, it will override the inherited setting for that one
    subtrack.


    An anomaly within the inheritance scheme is the "visibility" (display mode) 
    setting.  Unlike other settings, visibility is cumulatively restrictive from the
    supertrack level.  That is, if the parent has a visibility of  "dense" and the 
    child's visibility is
    "pack", the child will be displayed as "dense". If the parent is
    subsequently changed to "full" display mode, the child will now be shown in 
    "pack" mode.  At the trackDb
    level, default visibility is always cumulatively restrictive.
    However, when a user explicitly changes a subtrack visibility to be
    greater than what was inherited from parents, that subtrack's
    visibility will override the inheritance.  While the subtleties of
    inheritance can be hard to explain, they are often intuitive in
    practice.





    subGroup1 view <Views> <vTag1a=vTitle1a> [vTag1b=vTitle1b…]

    track <viewName>

    view <viewTag>
    A view is always declared both as a subgroup
    and in a track stanza itself.  The subgroup declaration is like
    previous declarations, but the view subgroup must have the tag
    view and be declared as the first subgroup.  Note
    that the view stanza follows the composite stanza with one level
    of indentation.  Subtracks will follow their view with an
    additional level of indentation.




    subGroups view=<vTag1>…

    parent <viewName> [off/on]
    A subtrack declares its membership in a view
    both as subgroup membership and with a parent setting that refers
    to the view track name.  Note that a track can only have one parent.  
    When the subtrack's parent is a view, the composite track is 
    its implicit grandparent.



viewUi on
    If subtracks within a view are configurable,
    then the view will have the configuration controls for it in a box
    beneath the view's visibility drop down.  That box filled with
    configuration controls is hidden by default so that the UI is not
    too cluttered.  The user must first open the box before its
    contents are seen.  If there is only one view with configuration
    settings, or if the view is the most important one, the box can be
    open by default.  Use this setting in the view stanza of settings
    to default the configuration box as open.



configurable <off/on>
    Tracks are configurable by default if their
    track type supports this, and views and composites are 
    configurable if their children's track type supports this.
    Finally individual subtracks are configurable by default
    if their track type supports it.  Sometimes it is desirable
    to turn off configuration.  Configuration may be turned back
    on when it has been turned off at a higher level. For example, this might be
    useful in a situation with a multi-view composite where the composite
    level would normally be configurable, but you want only one of the
    views and not all of the children of that view to be configurable.
    While this setting might be rarely needed, it can help restrict
    the user from viewing your data in inappropriate ways.



Example of a Composite track with Views
        track myMultiViewComposite
    compositeTrack on
    visibility dense
    subGroup1 view Views PK=Peaks SIG=Signals
    subGroup2 cell Cell_Line \
            A1GM12=GM12878 \
            CD14=CD14&#43; …
    subGroup3 ab Antibody \
            H3K04ME3=H3K4me3 \
            H3K36ME3=H3K36me3 …
    dimensions dimX=ab dimY=cell
    sortOrder cell=+ ab=+ view=+
    type bed 3
      ...

        track myViewPeaks
        parent myMultiViewComposite
        shortLabel Peaks
        view PK
        visibility pack
        type bigBed 6 +
        scoreFilter 0
        scoreFilterLimits 0:1000
        viewUi on
          ...

            track myFirstPeakSubtrack
            parent myViewPeaks on
            subGroups cell=CD14 ab=H3K04ME3 view=PK
              ...    
    The composite has two views, one of which is
    shown, along with a single subtrack belonging to that view.
    Notice that the view does not participate in the dimensions
    setting, as it is an implicit dimension controlled by a row of
    visibility dialogs at the top of the composite configuration page.
    Notice that the view does participate in the sortOrder setting
    like other subgroups.  In this example, the peaks view contains
    bigBed subtracks that all share the scoreFilter defaults
    defined at the view level.  Almost any setting that is common to
    the whole tree can be defined at the composite level; any setting
    that is common to the view can be set at the view level; and any
    setting that is specific to one subtrack should be set at that
    level.  Remembering inheritance, we 
    can see that the subtrack shown inherits its track type from
    the view, but has its default visibility limited by the composite.
    That is, it inherits packed visibility from the view but the
    composite will show all visible subtracks as dense.

    One additional thing to note is that this composite track is
    "type bed 3".  Composites do not need a type to define 
    their data format, since all data is associated with subtracks. Further, 
    multi-view composites almost always have multiple data formats.  
    But the "type" also controls what configuration options may be offered 
    for a track.  Typically, a single level composite has the same type as 
    all of its subtracks and offers user configuration options at the top 
    level. But a multi-view composite is most often given the bare-bones 
    "type bed 3", and offers user configuration options at 
    the view level.  Exceptions to this pattern do exist but they are rare.





Aggregate or Overlay Tracks: multiWig
    In some instances, data from multiple tracks is so closely
    related that it makes sense to view it as a single track.  The
    premiere example of this is the signal overlay
    track (i.e. "multiWig").  Signal overlay tracks display the signal
    data from several subtracks combined in several different ways, making it
    possible to see the data of several tracks together in a condensed
    view. The default overlay method for multiWigs is as colored transparencies,
    in which all the graphs are drawn on top of one other in such a way
    that overlapping regions are a different color. Another choice
    is solid overlay, where all the graphs are still drawn overlapping each
    other, but without transparency.  A third choice is stacked
    where the values of the subtracks are stacked on top of one another with
    no overlap such that the total height of the wiggle is the sum of 
    all the values in the subtracks.
    The value of the overlay track surpasses simply condensing the
    image.  Occasionally this is the most effective way to identify
    hidden relationships in the underlying data.  The overlay track
    should not be overused, however.  Attempts to overlay too many
    subtracks can hide important information as regions with many layered
    signals become too dark to interpret.  More than eight subtracks in a
    single overlay may prove less than ideal.  As with composites,
    it is important for the multiWig tracks to have the same data dimensions, 
    i.e. a signal height of 100 should be interpretable in the same
    way for the whole set of tracks.  While this is true for a composite
    or view, it is especially important for overlay tracks.  You cannot
    reasonably overlay a signal from 0-1 with another signal from 0-1000.



container multiWig
    Signal overlay tracks are declared much like
    simple composites.  However, instead of a "composite"
    setting, they declare themselves as a "container" of
    "type multiWig".  Like simple composites, all subtrack
    types should be identical and the container itself should be
    declared as the same type (e.g. "bigWig").  Also like a composite,
    the container parent should have common settings for all children.
    Unlike composites, containers can have neither subgroups nor
    views.  Additionally, all subtracks within a container are configured as one; 
    there is no independent configuration of individual subtracks.  Even when the user
    sets the overlay method to none and the subtracks are viewed as
    separate signals, they are still configured as a set.



parent <containerTrack>
    Membership in a container track is declared at
    the subtrack level.  The subtracks should be defined with indent
    beneath their container parent.



aggregate <transparentOverlay/stacked/solidOverlay/none>
    It is important to declare an aggregation method; otherwise, this set of tracks displays 
    as a composite would, with additional restrictions. Of the four options, the preferred 
    setting is transparentOverlay. The setting stacked
    will draw the graphs in stacked mode.
    The setting solidOverlay should not be used if there
    are more than a couple of tracks, and none should never be the
    default.  The aggregation method is a configurable option,
    however, so the user may wish to temporarily set it to none in
    order to see subtleties hidden in overlay mode.



showSubtrackColorOnUi on
    Subtracks in an overlay have individual colors.  Use this setting to show the color 
    associated with each on the track configuration page.



Example of an Aggregate track
        track myMultiWig
    container multiWig
    aggregate transparentOverlay
    showSubtrackColorOnUi on
    type bigWig 0 1000
    viewLimits 0:10
    maxHeighPixels 100:32:8
      ...

        track myFirstOverlaySig
        table myFirstWig
        parent myMultiWig
        color 255,128,128
        wig 0 1139
          ...

        track myFirstBigWig
        parent myMultiWig
        color 120,235,204
          ...    
    This container is for a transparent overlay of
    signal tracks with 2 subtracks shown.  The tracks are
    of type "bigWig", though the first subtrack is a wig.
    Such mixtures are allowed.  Notice that the wig has a slightly
    larger range than the others.  The signal dimensions are close
    enough in this case, and the default viewLimit applied to all
    subtracks suggests that any signal above 10 is interpreted as
    strong. Note that each subtrack must define its color, and
    in this example, that color will be seen in the track
    configuration page as well as in the image.  Also notice that the
    first subtrack declares a table as distinct from its track name.
    Usually the table (or remote file root) name is the same as the
    track name.  The track name is a unique key.  But it is frequently
    the case that a table or remote data file may be displayed as an
    individual track or subtrack, as well  as part of a signal overlay
    track.  Setting the table name here suggests that a track named
    "myFirstWig" also exists and is displaying the same data used in
    this overlay track.



Example of an Aggregate track
        track myMultiWig
    container multiWig
    aggregate transparentOverlay
    showSubtrackColorOnUi on
    type bigWig 0 1000
    viewLimits 0:10
    maxHeighPixels 100:32:8
      ...

        track myFirstOverlaySig
        parent myMultiWig
        color 255,128,128
        type bigWig 0 1139
          ...

        track myFirstBigWig
        parent myMultiWig
        color 120,235,204
          ...    
    This container is for a transparent overlay of
    signal tracks with 2 subtracks shown.  The tracks are
    of type "bigWig".  Notice that the first subtrack has a slightly
    larger range than the others.  The signal dimensions are close
    enough in this case, and the default viewLimit applied to all
    subtracks suggests that any signal above 10 is interpreted as
    strong. Note that each subtrack must define its color, and
    in this example, that color will be seen in the track
    configuration page as well as in the image.




Custom Tracks
    NOT FOR HUBS.
    Custom tracks are
    tracks that get loaded into the Browser through the hgCustom CGI.
    Unlike locally hosted tracks, or even Data Hub tracks, they do not
    have a trackDb.ra  stanza to define their format and behavior in the
    Browser.   Nevertheless, they will support most of the settings as a
    locally hosted track of the same type.  There are a few additional
    settings that are needed to fully support custom tracks.



genome
    Filled with genome/assembly db name.



offset
    Used only once, to apply an offset to bed
    type data of a custom track.



browserLines
    Internal only – user does not set.
    Filled with all trackDb.ra style lines from
    hgCustom input.



dataUrl
    Internal only – user does not set.
    Filled if custom tracks is loaded via URL.



dbTrackType
    Internal only – user does not set.
    
Not sure how it is distinguished from
    tdbType.



fieldCount
    Internal only – user does not set.
    Filled with number of bed columns as
    determined in hgCustom CGI.



firstItemPos
    Internal only – user does not set.
    Filled with first bed item in bedList in
    hgCustom CGI.



htmlFile
    Internal only – user does not set.
    Filled with name if trash file that contains
    HTML description for custom track.



htmlUrl
    Internal only – user does not set.
    Filled with user entered URL for track
    description in hgCustom CGI.



initialPos
    Internal only – user does not set.
    Filled with position from hgCustom input.



inputType
    Internal only – user does not set.
    Filled with custom factory name as
    determined in hgCustom CGI.



itemCount
    Internal only – user does not set.
    Filled with bed item slCount in hgCustom
    CGI.



mafFile
    Internal only – user does not set.
    Filled with name of trash file that contains
    maf data as loaded in hgCustom CGI.



maxChromName
    Internal only – user does not set.
    Obsolete: Filled with minimum index size for
    db that won't "smoosh" together chromNames.



origTrackLine
    Internal only – user does not set.
    Filled with "track" line as entered by user
    in hgCustom CGI.



tdbType
    Internal only – user does not set.
    
Holds the type that should go into
    tdb->type.



wibFile
    Internal only – user does not set.
    Filled with name of trash file that contains
    wib binary data as loaded in hgCustom CGI.



wigFile
    Internal only – user does not set.
    Filled with name of trash file that contains
    wig data as loaded in hgCustom CGI.

Specialized or rarely used types:

Rejected "types":

List of Miscellaneous Specal Case, Deprecated, Rejected or Rarely Used Settings

Track Database Definition

How to declare Dataset Display Settings in the Genome Browser

Hub Track Database Definition

How to declare Dataset Display Settings in Genome Browser Hubs

Common, though less frequently used settings

bed/bigBed: Item or region tracks

bigBed: Item or region tracks

wig, bigWig, and bedGraph: Signal graphing tracks

bigWig: Signal graphing tracks

genePred: Gene models and predictions

bam: Compressed Sequence Alignment/Map tracks

psl: Sequence alignments

chain and netAlign: paired species alignments

wigMaf: Multiple alignments

expRatio: Microarray expression data

snpNNN: specialized subclass of BED 6 for dbSNP variants

vcfTabix: Variant Call Format indexed by tabix

pgSnp: Personal Genome SNP format

altGraphX: Alternate splicing gene model tracks

bedDetail: Text extended bed track

clonePos: Genome coverage tracks

ctgPos: Physical map contigs tracks

downloadsOnly: Specialized track that contains only downloadable files

encodeFiveC: Five C Chromatin interaction track

factorSource: Combined items tracks

rmsk: Repeat masking tracks

snake: Self referencing alignment tracks - EXPERIMENTAL

Predefined major track groupings

Supertrack settings

Composite Tracks

Composite Tracks

Subgroups

Views

Aggregate or Overlay Tracks: multiWig

Custom Tracks