Hi Jessica, In your BED output from your table browser intersection, the number you are seeing in the 9th column is a decimal representation of the R,G,B, value. The R,G,B, value is converted to a single number for storage in the database. See this fun web site for more info on how this is done: http://www.mathsisfun.com/hexadecimal-decimal-colors.html.
In order to have the browser interpret these numbers correctly and display the colors, when you upload your BED output as a custom track, add itemRgb='On' to the track line and you should see your colors. Or instead of "BED - browser extensible data" as your output format of your intersection, select "custom track." When prompted click "get custom track in table browser." Then from the table browser page, click "manage custom tracks." Click on the title of you new output custom track to update it and add itemRgb='On' to the track line and click submit. When you view your new custom track in the browser, it should have your colors. I hope this is helpful! Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Jessica Wasserscheid wrote, On 3/18/2011 8:02 AM: > Hi, > > I am working on the following session : > http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Jwassers%20mcgill&hgS_otherUserSessionName=jcrary_TOD_study.hap2 > > When using the Table browser to intersect in Custom Tracks > *1059.snps* > chr17_ctg5_hap1 759070 759071 T 1000 . 759070 759071 > 87,87,87 > chr17_ctg5_hap1 761175 761176 C 1000 . 761175 761176 > 87,87,87 > chr17_ctg5_hap1 764678 764679 A 1000 . 764678 764679 > 87,87,87 > *with* > *H2>H1 diff > *I lose the color (9th column) in the BED output. Actually it is > replaced with a number that I don't understand : > > chr17_ctg5_hap1 758728 758729 C 1000 . 758728 758729 > 2631897 > chr17_ctg5_hap1 758788 758789 G 1000 . 758788 758789 > 2631897 > chr17_ctg5_hap1 759070 759071 T 1000 . 759070 759071 > 2631897 > chr17_ctg5_hap1 759070 759071 T 1000 . 759070 759071 > 5723991 > > Any help would be appreciated, > > Thanks > Jessica > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
