- Genome Browser
- My Data
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. In fact, an attempt to load a bedGraph custom track over 50,000,000 lines
will result in an error message, but can be addressed by turning the bedGraph into a bigWig (see
Example 3). Note that bedGraph files cannot easily be converted to
wiggle files; converting bedGraph to bigWig and using
bigWigToWig will return the
original bedGraph file.
The bedGraph format is line-oriented. BedGraph data are preceded 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
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 must remove the line breaks.
The track type is REQUIRED, and must be 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.)
BedGraph track data values can be integer or real, positive or negative values. The chromosome coordinates are zero-based, half-open. This means that the first chromosome position is 0, and the last position in a chromosome of length N would be N - 1. The positions listed in the input data must be in numerical order, and only the specified positions will be graphed. bedGraph format has four columns of data:
chrom chromStart chromEnd dataValue
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
The above example is a custom track that includes a
track type= line that is
specific for loading the data in the browser. This line will cause a raw bedGraph data file to fail
validation by other tools, such as
validateFiles, outside of the browser.