JASPAR track settings

[Никита Геннадьевич Созонов]

Hello

I'm trying to find a way to configure JASPAR track to filter items by several TFBS names. Is it possible?

Thank you!

Nikita

[Daniel Schmelter]

Hello Nikita,

Thank you for contacting the Genome Browser and for your interest in the JASPAR hub tracks.

The JASPAR data comes from a Public Track Hub, which is externally configured. It appears that they have not enabled the input of multiple name items from the configuration page. This is a relatively simple addition, which you can request they add if you so wish. If you do contact them, request they add the labelSeparator and include this link:

http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html#labelFields

The workaround to this is to use Table Browser's "Identifiers" filter to query the JASPAR track for a list of names separated by newlines. This will return data where the names match any of the identifiers you enter. By default, this output is in a text file, but you can view it in the Genome Browser by selecting the output format dropdown labeled "Custom Track" and then clicking "get custom track in Genome Browser". Note that due to the extreme size of the JASPAR 2020 track, at 12 billion data lines, the query may take a few seconds and it will not work on genome-wide searches. Here is a link that will take you to the JASPAR hub Table Browser view on hg19:

http://genome.ucsc.edu/cgi-bin/hgTables?hgS_doOtherUser=submit&hgS_otherUserName=dschmelt&hgS_otherUserSessionName=JASPAR.TB

I hope this was helpful. If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

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