Advanced UCSC Genome Browser Features: webinar follow-up

We will have had our second webinar on the UCSC Genome Browser on May 26th. It is an introduction to many of the advanced features and display aspects of the browser. It corresponds to the material that you can find on our UCSC-sponsored tutorial materials that are freely available here: http://www.openhelix.com/ucscadv

We will have had some time for some questions at the webinar. But there may be things we didn’t have time to discuss, or cover in enough detail. Or people may go away and try some things and then come back with further questions. This thread will serve as a place to discuss issues around the Advanced materials, the webinar, browser basics, etc. We’d also love to hear any feedback on other things you’d like to see covered in the future as well.

Some of the links used in the webinar:

UCSC Genome Browser
UCSC Tutorial (slides, movie, handouts, exercises)
UCSC Mailing Lists
Additional OpenHelix Tutorials
RepeatMasker (in answer to a question about masked repeats)
Genomics Glossary (in answer to a question about a good glossary)
LiftOver (in answer to a question about how to convert sequence between assemblies)

What did you think? Do you have questions or comments? Let us know!

6 thoughts on “Advanced UCSC Genome Browser Features: webinar follow-up

  1. Jennifer Post author

    From ekorvatska:

    For intersections: if you want to include introns , not only exons how to do this?

  2. Jennifer Post author

    From Oleksiy Karpenko: Could you explain who wig signals are stored in the tables and how to query them in Table Browser?

  3. Jennifer Post author

    From Scott7: i saw on the website i think a third tutorial? is that a webinar?

  4. Mary

    On the “super tracks” question: an example of a track that combines several types of data into a larger set can be found on the Mar 2006 assembly, in the “Regulation” group. Find the link called “ENCODE Regulation” and click that, or use this link:

    http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=196569961&c=chr5&g=wgEncodeReg

    In the News Archives (http://genome.ucsc.edu/goldenPath/newsarch.html) you can see an item about the super-track 20 August 2010.

    We’ve been told it’s not possible yet for users to create those, but we will bring that interest to the folks at UCSC. We’ve heard that more than once, it’s nice to see people would like that.

  5. Trey

    One way to include the entire gene region (not just exons/utrs) in a search, is to define regions or use gene IDs in the search instead of an intersection.

    Choose Simple Repeats (or dataset you are interested in), then either define regions if you know the gene regions of interest, or paste/upload a list gene IDs.

    This will search the entire gene region, utr/intron/exon and return items for entire region.

    If you wanted to limit it to just exons/utrs, then do the search above, but this time interesect with knowngenes (or refseq, etc) with overlap. If you wanted to search just introns, do same intersection, only this time say “no overlap”

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