[Genome] Custom tracks on UCSC genome browser

[Rachel Harte]

Hello Kim,

If you create a BED format file for the custom track, you can use the
itemRgb field to specify a color for each item in the track. The track
line itemRgb attribute must be set to "On". This will determin the color
for the data in this line of the BED file. You will need to add values for
the 8 fields preceding this one. The BED format is described here:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED

Example 5 at the bottome of the BED lines section shows how this is done.

More information about creating custom tracks and examples are here:
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#BED

If you are specifying one gene per BED file line then the color will only
apply to that whole gene. In order to get exons colored differently, you
will need to create a separate BED format line for each exon and specify
an itemRgb value in each line. This tye of display would not show gene
structure, you would just see blocks of exons with no line representing
the introns to join the exon blocks together to form a gene. You could add
extra lines to the BED format file to specify the intron positions and
set their color to gray or black. This way, the gene structure would still
be preserved.

I hope that this helps you. Please let us know if you have further questions.

Rachel

Rachel Harte
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


On Tue, 5 Dec 2006, Kim Wong wrote:

> Hello,
>
> I was wondering if it is possible to create a custom track with blocks
> on the same track colored differently. Eg: different exons of a gene.
>
> Thanks,
> Kim
>
>
> Computational biologist
> Genome Sciences Centre, BC Cancer Agency
> Vancouver, BC. Canada
> 604.877.6000 x3265
> kwong at bcgsc.bc.ca
> _______________________________________________
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