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Video Tip of the Week: UCSC Table Browser and Custom Tracks

UCSC IntroThis week’s video tip is longer than usual. But if you want to dig deeper into all the data that you know is coming in to the UCSC Genome Browser, you want to use the Table Browser. If you’ve only used the genome browser interface, you are missing a lot of opportunity to mine for great data.

The UCSC Genome Browser folks have been continuously adding new features and data over the years since they’ve been sponsoring our free training materials. But the look of the Table Browser hadn’t changed all that much. However, with the move to the new hg38 assembly as the default human genome, it was a good time for us to update the shots of the training materials for the Table Browser. It also gave us the chance to include track hubs, which we hadn’t covered in the previous version. And we also touch briefly on Genome Browser in a Box.

As before, we have a recorded video. And we have also included updated slides that you can use to train others. And our exercises are there for more practice, too.

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We’ve also mentioned before that we have a handy paper that also can help people to get up to speed on UCSC features. Our Current Protocols paper is now un-paywalled in PMC, so if you want to supplement the video with this other piece, there’s a bit more detail on how to do hubs of your own. But you should also see the specific papers on that. And there’s more guidance in this video tip from before.

So check out the new materials for the advanced topics. And see the new preprint (linked below) for more details and upcoming features as well.

Quick links:

UCSC Genome Browser homepage: genome.ucsc.edu

Training suite: openhelix.com/ucscadv

References:

Rosenbloom, K., Armstrong, J., Barber, G., Casper, J., Clawson, H., Diekhans, M., Dreszer, T., Fujita, P., Guruvadoo, L., Haeussler, M., Harte, R., Heitner, S., Hickey, G., Hinrichs, A., Hubley, R., Karolchik, D., Learned, K., Lee, B., Li, C., Miga, K., Nguyen, N., Paten, B., Raney, B., Smit, A., Speir, M., Zweig, A., Haussler, D., Kuhn, R., & Kent, W. (2014). The UCSC Genome Browser database: 2015 update Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku1177

Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steve Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent. (2015). The UCSC Genome Browser database: 2016 update bioRxiv DOI: 10.1101/027037

Mangan ME, Williams JM, Kuhn RM, & Lathe WC (2014). The UCSC Genome Browser: What Every Molecular Biologist Should Know Current Protocols in Molecular Biology., 107 (19.9), 199-199 DOI: 10.1002/0471142727.mb1909s107

Disclosure: UCSC Genome Browser tutorials are freely available because UCSC sponsors us to do training and outreach on the UCSC Genome Browser.