Colors in the GenePred track
Nowoshilow,Sergej
Dear UCSC genome browser support,
For our axolotl genome project, I set up a UCSC Genone Browser instance and loaded the annotation tracks in GenePred format.
However, there are several types of genes we have – complete genes, partial genes and putative pseudogenes. I was wondering if it is possible to color each entry in a GenePred file separately depending on its type. The format itself does not have a designated field for that. However, I know that I can color each item in a bigGenePred file. I didn’t find a way to load a bigGenePred file into the local DD, though. If I understand it correctly, bigGenePred files have to be served from an external/internal resource via HTTP.
In principle, I could a BED12-formatted file for the gene prediction track, but I don’t know if there could be any disadvantages.
Another solution I have come up with is to load a separate track for each type of the genes, but it’s a bit ugly…
Thanks for any advice!
Best,
Sergej
Dr. Sergej Nowoshilow
Post-doc in Tanaka Lab
Elly Tanaka group, IMP
Animal models of regeneration
email: Sergej.N...@imp.ac.at
phone: +43 (0) 1 79730 3203
orcid: 0000-0001-8360-5010
IMP
Research Institute of Molecular Pathology
Campus-Vienna-BioCenter 1
1030 Vienna, Austria
Part of Vienna BioCenter
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Jairo Navarro Gonzalez
Hello Sergej,
Thank you for using the UCSC Genome Browser and sending your inquiry.
You can use the "reserved" field to color each item in a different color depending on the type. The reserved field is defined in the on the bigGenePred format description page, https://genome.ucsc.edu/goldenPath/help/bigGenePred.html#bigGenePred. When creating the bigGenePred track for a track hub, you can point to the file by using the "bigDataURL" parameter to specify the external URL to the file or the relative path on the server. You can learn more about this parameter from the trackDb help page, https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#bigDataUrl.
The following session is an example of a bigGenePred file that uses different colors for each item, https://genome.ucsc.edu/s/jnavarr5/hg38.Holiday_Tree. The underlying files for the track hub can be found in the following directory, https://hgwdev.gi.ucsc.edu/~jairo/trackHubs/MLQ_24739/.
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Jairo Navarro
UCSC Genome Browser
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Nowoshilow,Sergej
Hi Jairo,
Thanks for the quick response!
I would like to avoid using bigGenePred, though. I saw that it is possible that’s why I was wondering if one could do the same with the regular GenePred. The reason I would like to stick to the local files is that setting up a trackhub would add another layer of complexity such that I either have to set up a dedicated VM for that purpose only or serve the trackhub data from the same VM that runs the Genome Browser – therefore, the VM would serve the data to itself, which is a bit confusing. Do you see what I mean?
With the regular GenePred file, I can import the data into the DB, make the track searchable etc, which is quite convenient for me.
Do I get your point correctly that I can only color individual items in bigGenePred, but not in GenePred? In this case I either have to add several GenePred tracks and specify the color in the trackDb.ra file or use BED12 instead of GenePred.. is this correct?
Thanks and have a nice weekend!
Daniel Schmelter
Hello Sergej,
Thank you for your patience with this process.
You are correct in saying that genePred will not be suitable to color your regions. The fields in genePred are do not include the Reserved RGB field in column 9 that exists in bigGenePred. The binary compressed bigGenePred is similar to a bigBed file in that it does have a Reserved RGB field and will be suitable in the same way my colleague Jairo mentioned. To be clear, you would not have to set up a Track Hub to display bigGenePred files, you could instead display your data as a Custom Track using the following format:
track type=bigGenePred itemRgb="on" baseColorDefault=genomicCodons bigDataUrl=https://hgwdev.gi.ucsc.edu/~jairo/trackHubs/MLQ_24739/hg38/bigGenePred.bb
If you have already set up a Genome Browser mirror on a virtual machine, you do not need to set up an additional VM to host your data and can simply create a local URL. For GBiB, you can add a "shared folder" to generate local file urls like http://127.0.0.1:1234/myfile. If you have not set up a Browser mirror, you can refer to our data hosting section:
http://www.genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Hosting
If you really prefer text format, it may be best to use the BED12 text format for your data. This format allows for color specification and you can make it searchable by using a method similar to the one described for Track Hubs here, but uploading using a custom track instead:
https://genome.ucsc.edu/goldenPath/help/hubQuickStartSearch.html
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, please send it instead to genom...@soe.ucsc.edu.
All the best,
Daniel Schmelter
UCSC Genome Browser
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/C3CC71DD-EADC-420F-8D42-A34EBB02BA5A%40imp.ac.at.