Question about generating trackDb.txt for Track Hubs

[Qianhui Wan]

Hello,

I have a question about generating trackDb.txt from hub.txt and genomes.txt. I remember there being a function documented on the UCSC tutorial pages that handled this automatically. However, I can no longer find it.

Is this referring to the trackhub function/package? If so, could you please point me to the correct website or documentation that shows the relevant code?

Thank you so much for your help.

Best regards,

Qianhui Wan

Email: qw...@coh.org

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

We do not have a command-line utility to generate a trackDb file for you, but we do have help pages with a template you can update for your research. For example, the following pages help explain how to create a track hub:

Hub Basics: https://genome.ucsc.edu/docs/hubs/hubBasics.html
Track Hub Quick Start Guide: https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

If you are interested in learning about the different trackDb functions that can be used in your track hub, please refer to the following definitions page:

https://genome.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html

You may also be interested in using the "useOneFile on" setting, which lets you use a single file for hub.txt, genomes.txt, and trackDb.txt. The only limitation for this setting is that the trackHub can only be for one genome assembly.

https://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#UseOneFile

We are also offering hosting space for every user, and you can upload a bigBed, bigWig, BAM, VCF, etc directly to the UCSC Genome Browser. This feature is still under development, so any feedback or bug reports are appreciated. You can find this feature under the "Hub Upload" tab for the track hubs page:

https://genome.ucsc.edu/cgi-bin/hgHubConnect#hubUpload

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.

Jairo Navarro
UCSC Genome Browser

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