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The bedGraph format allows display of
continuous-valued data in track format. This display type is
useful for probability scores and transcriptome data.
This track type is similar to the wiggle (WIG) format,
but unlike the wiggle format, data exported in the bedGraph format
are preserved in their original state.
This can be seen on export using the table browser.
For more details on data compression in wiggle tracks see the
notes section of the wiggle
track description page.
If you have a very large data set and you would like to keep it
on your own server, you should use the
bigWig data format.
General Structure The bedGraph format is
line-oriented.
Bedgraph data are preceeded by a
track definition line, which
adds a number of options for
controlling the default display of this track.
Following the track definition line are the
track data in four column BED format.
chromA chromStartA chromEndA dataValueA
chromB chromStartB chromEndB dataValueB
Parameters for bedGraph track definition lines
All options are placed in a single line separated by spaces:
track type=bedGraph name=track_label description=center_label
visibility=display_mode color=r,g,b altColor=r,g,b
priority=priority autoScale=on|off alwaysZero=on|off
gridDefault=on|off maxHeightPixels=max:default:min
graphType=bar|points viewLimits=lower:upper
yLineMark=real-value yLineOnOff=on|off
windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16
(Note if you copy/paste the above example, you have to remove the carriage returns.)
The track type is REQUIRED, and must be bedGraph:
type=bedGraph
The remaining values are OPTIONAL. The wiggle documentation contains details on these options.
A functional description of these options can be
seen in the track configuration description. (Custom tracks do not
have interactive configuration options.)
Data Values
Bedgraph track data values can be integer or real,
positive or negative values. Chromosome positions
are specified as 0-relative. The first chromosome
position is 0. The last position in a chromosome
of length N would be N - 1. Only positions specified
have data. Positions not specified do not have
data and will not be graphed. All positions specified
in the input data must be in numerical order.
The bedGraph format has four columns of data:
chrom chromStart chromEnd dataValue
Note: These coordinates are
zero-based, half-open.
Example
This example specifies 9 separate data points in three
tracks on chr19 in the region 49,302,001 to 49,304,701.
To view this example as a custom track in the Genome
Browser, copy the text and paste it into the browser annotation track text box.
browser position chr19:49302001-49304701
browser hide all
browser pack refGene encodeRegions
browser full altGraph
# 300 base wide bar graph, autoScale is on by default == graphing
# limits will dynamically change to always show full range of data
# in viewing window, priority = 20 positions this as the second graph
# Note, zero-relative, half-open coordinate system in use for bedGraph format
track type=bedGraph name="BedGraph Format" description="BedGraph format" visibility=full color=200,100,0 altColor=0,100,200 priority=20
chr19 49302000 49302300 -1.0
chr19 49302300 49302600 -0.75
chr19 49302600 49302900 -0.50
chr19 49302900 49303200 -0.25
chr19 49303200 49303500 0.0
chr19 49303500 49303800 0.25
chr19 49303800 49304100 0.50
chr19 49304100 49304400 0.75
chr19 49304400 49304700 1.00
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