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GMOD is a set of interoperable open source software components for visualizing, annotating, and managing biological data. See http://gmod.org for more.

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[Istvan Nagy]

Hi !

I have a large BED file of about 1 million lines and I would like to show different feature types with different colors in GBrowse.
My BED file contains RGB color codes like 60,105,225 in Column 9 - which column is dedicated to colors according to the BED specifications:
"9. itemRgb - an RGB colour value (e.g. 0,0,255). Only used if there is a track line with the value of itemRgb set to "on" (case-insensitive)."
Is there any way in GBrowse to set that "itemRgb" value ?
All my features are presently shown in orange.
Thanks
(Sorry for bothering you if this is not the right forum for such naive questions, but I was unable to find a better (and working) option ... )

[Scott Cain]

Thankfully, Sourceforge sent me an email about this post, or I certainly would have never seen it :-)

I tried to send this message to the GBrowse mailing list, but using your Sourceforge email address bounced. Here's what I wrote. If you want to respond, please do so on the mailing list (gmod-gbrowse@lists.sourceforge.net):

Can you tell me a little more about what you are doing? Do you have administrative control of this GBrowse instance? If not, I don't think you have any way of changing the display color for a BED file. However, if you convert it to a "Feature File Format" (which I believe is specific to GBrowse--I don't recall seeing this format anywhere else), you can more control over how features are displayed. Of course, since you have a pretty large BED file, converting would require some sort of scripting. See https://wormbase.org/gbrowse-static/annotation_help.html for more information (this page is installed with every GBrowse instance as part of the help docs).

If you have administrative control (that is, you run the GBrowse server), then you have more options, outlined here:

http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks

though it's not clear to me that the wiggle processing script will respect the column 9 data. In this case, it would probably make more sense to convert to GFF3 and use perl callbacks in the configuration to do the coloring.

Scott