Bedgraph colors
shruti sinha
I'm trying to visualize CNV data in UCSC.
I was hoping to use the bedgraph to visualize the copy numbers for the CNVs as it plots bargraph. So basically i would like to see if there is concordance between the CNV calls and the copy number called by the two different programs.
For this I would like to color the regions based on the calls and the copy number as the bargraph.
is there any track format or any of the track settings which could help me do such a visualization?
thanks in advance
shruti
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Steve Heitner
Hello, Shruti.
The bedGraph format does not offer the functionality to specify colors as you describe. You can view the bedGraph specification page at http://genome.ucsc.edu/goldenPath/help/bedgraph.html. Items in a bedGraph track will only appear in two colors: one color for values greater than or equal to zero and one color for values less than zero.
The BED format offers more flexibility as far as coloring goes. You can view the BED specification page at http://genome.ucsc.edu/FAQ/FAQformat.html#format1. You should pay special attention to the “score” and “itemRgb” fields. You can see an examples of both just below the BED field descriptions. The only drawback to this format is that it does not represent the data in bar graph format as you described.
Please contact us again at gen...@soe.ucsc.edu if you have any further questions.
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Steve Heitner
UCSC Genome Bioinformatics Group
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