How do I get the names of the various native tracks that can be used in a hgTracks link?
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Endre Bakken Stovner
Sep 7, 2016, 10:16:32 AM9/7/16
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First: thanks for the genome browser. It has helped immensely in understanding our timeseries ChIP-Seq project.
Anyways, my question is the following:
I have a link to download a graph from UCSC that looks like the following:
As you can see, there are many native tracks listed in the link like wgRNA, wgEncodeReg, cpgIslandExt etc. Do you have a list somewhere of all the tracks available for use in a link like this? Preferably a file that has a mapping between the name/description of a track and the name to use in a link.
If I need to parse webpages or recurse an ftp to find the filenames that is fine too, although obviously less preferable.
Thanks!
Matthew Speir
Sep 9, 2016, 2:23:08 PM9/9/16
to Endre Bakken Stovner, UCSC Genome Browser Discussion List
Hi Endre,
Thank you for your question about obtaining track and table names.
You can obtain this information using the "tableName" and "shortLabel" columns in the trackDb table that is available for every assembly. You can download the contents of this table from our download server, http://hgdownload.soe.ucsc.edu/downloads.html, under the "Annotation database" link for your assembly of interest. The tableName and shortLabel columns represent the 1st and 2nd columns in the table, respectively.
Note that in some cases, tables mentioned in the "tableName" column aren't true tables but are rather super or composite track containers into which other tracks are placed. One example is the cpgIsland* tracks:
As you can see there is a "cpgIslandSuper" track, which in this case is the super track container for the other two cpgIsland* tracks. In this case, it's somewhat obvious which one is the super track container and which ones are the true tables containing the data, but this may not be the case for every super or composite track.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
Thank you for your question about obtaining track and table names.
You can obtain this information using the "tableName" and "shortLabel" columns in the trackDb table that is available for every assembly. You can download the contents of this table from our download server, http://hgdownload.soe.ucsc.edu/downloads.html, under the "Annotation database" link for your assembly of interest. The tableName and shortLabel columns represent the 1st and 2nd columns in the table, respectively.
Note that in some cases, tables mentioned in the "tableName" column aren't true tables but are rather super or composite track containers into which other tracks are placed. One example is the cpgIsland* tracks:
tableName shortLabelcpgIslandExt CpG IslandscpgIslandExtUnmasked Unmasked CpGcpgIslandSuper CpG Islands
As you can see there is a "cpgIslandSuper" track, which in this case is the super track container for the other two cpgIsland* tracks. In this case, it's somewhat obvious which one is the super track container and which ones are the true tables containing the data, but this may not be the case for every super or composite track.
I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
Matthew Speir
UCSC Genome Bioinformatics Group
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