Hello Tien-chi, This is possible, but you will need to use bigBed format instead of bedGraph. http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
To color as you request, the data will have to specify the color for each item/line (rather than have color/alt-color assign color). The original BED file used as input should have all of the first nine attributes specified or filled with acceptable placeholders, with the exception of the ninth field which must be an assigned color (itemRgb). bed file description: http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED or http://genome.ucsc.edu/FAQ/FAQformat.html#format1 big BED file description, including instructions for transforming a bed file to bigBed. See example 3 for a nine column BED file used as input: http://genome.ucsc.edu/goldenPath/help/bigBed.html Then, for the track line: 1) Do not use the color attribute in the track line so that it defaults to black. 2) Set itemRgb=On to interpret the itemRgb values 3) Use bigDataUrl (the file must be located on your own server) We hope this helps, Jennifer On 3/17/10 9:44 PM, Tien-chi Pan wrote: > Hi, > > I am using the following track definition line to display copy number data > in two-color BedGraph: > > track type="bedGraph" name="Track1" description="Track 1" visibility=full > color=255,0,0 altColor=0,255,0 autoScale=off viewLimits=-2:2 > > All is fine except the track label shows up as red due to the color > parameter setting. The effect I would like to achieve is having red bars for > positive data and green bars for negative data, while the track label > remains black. > > Is there a way to set the color of the track label separately from the > colors of the bars? I tried setting itemRgb but it didn't appear to work on > BedGraph. > > Thanks, > Tien-chi > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
