A couple of IGB users asked us about configuring color settings using track lines in GFF format files. Here is a representative question:
I am trying to automatically generate certain annotation files in gff3 format. During this process I want to customize the color. Through the release notes of earlier versions of IGB and the documentation, I was able to see that you accept ucsc-style track lines for gff3 files (with ##track directive).
Unfortunately, the color tag seems to be ignored in the newest IGB version (9.0.2).
If I use the following example (tab separated with empty attribute):
##track name="test" color=230,115,200
NC_002163.1 . nucleotide_motif 1 3 . + .
NC_002163.1 . nucleotide_motif 122 124 . + .
The track will be named "test" but the color is ignored.
I have tested many different variations, but I was unable to add custom color via the track line. I tested track lines from your documentation and they did not work either.
If this is not a bug, could you please tell me how this works?
We looked into this and realized that due to how track style information gets propagated in IGB, that there is currently no way to set the color of a track using the GFF header. So, unfortunately, there is no way to do this, currently.
We have been looking into a fix but so far don't have a solution as yet!
See also: https://jira.transvar.org/browse/IGBF-1835