Colors of tracks in UCSC
Saroja Somasundaram
Hi,
Thanks for your support with UCSC.
I have another users saved session in UCSC with different colors for different tracks. I would like to get the colors list for this session as a single file without having to click each track. Is there a way to download the track name and its respective color as a text file for a session?
Thanks,
Saroja
Daniel Schmelter
Hello Saroja,
Thank you for using the Genome Browser and for your question about extracting color information from Custom Tracks.
There are a few things that affect color, depending on the track type. To provide the most specific answer, it would be helpful if you could share a session to your Browser view with your Custom Tracks loaded (http://genome.ucsc.edu/goldenPath/help/hgSessionHelp.html#Share). I will provide a few answers for finding color values for the most common data coloring in the Browser.
For BED, GTF, and genePred Custom Tracks, there is no way to bulk extract the colors from each track. These Custom Tracks have color added with a 'color' or an 'altColor' setting included in the track line, as documented in the TrackDb page (http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#color). You can access that information for each track by going into the Custom Track Management page (http://genome.ucsc.edu/cgi-bin/hgCustom) and clicking the link in the 'Name' column. This will take you to the track line, which will include the color setting if it exists.
For bedGraph, wig, and bigWig Custom Tracks. You can view the color code of a wig track by using the Track Collection builder tool (http://genome.ucsc.edu/cgi-bin/hgCollection). After creating a new collection, click the plus sign next to the native wig tracks to add that track to your collection. You can get the color by double-clicking the track name within your collection to edit the track information. This "Edit Track" pop-up has the color used by the track in hexadecimal. For example, on hg38, the ENCODE track, H3K27Ac Mark (Often Found Near Regulatory Elements) on GM12878 Cells from ENCODE, uses the color #ff8080. This can be converted to RGB using an online tool (such as https://www.rapidtables.com/convert/color/hex-to-rgb.html).
If the track items are individually colored with an 'itemRgb' or 'score' column, it may be possible to bulk download these color values with Table Browser, but only one track at a time. It is difficult to speculate without knowing what data you are looking at. If you would like further assistance, could you please share a session link?
I hope this was helpful. If you have any more questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Daniel Schmelter
UCSC Genomics Institute
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