Is there a way to hide/collapse (intron) regions in the genome browser?

[Shawn McClelland]

I like the ability to put my own custom tracks on here and use it to visualize locations of things on a gene, or the genome. But one thing that keeps happening is that with larger genes and genes with huge introns the visualization kind of breaks down to tiny little tick marks of exons and 'annotations'.

I would love it if some how I could choose to fold up/hide/collapse regions so that all I am seeing is exons with breaks. I was really hoping the genome browser would allow me NOT to have to make my own web app or local app for such visualization :).

Is this type of thing possible? Are there other, easy suggestions for doing what I am talking about?

Thanks,

  Shawn

[Jonathan Casper]

Hello Shawn,

Thank you for your question about viewing only exons within the UCSC Genome Browser. We do not have a display mode that matches what you are describing, where you can collapse regions of the genome to view two (or more) remote pieces next to each other in detail. I will pass that feature request along to our development team.

In the interim, however, you may be interested in our previous/next exon navigation buttons. When your browser view is zoomed in to view only part of a gene, small double arrows will appear at the left and/or right edges of the gene in the browser window. Hovering over these arrows will display "next exon" or "previous exon" along with the exon count, and clicking them will jump your browser view to that exon. If you do not see the arrows, you might have the feature turned off. You can reach the configuration page by clicking "configure" beneath the track image of our browser, or by clicking "configure tracks and display" on our gateway page at http://genome.ucsc.edu/cgi-bin/hgGateway. Make sure the box next to "Next/previous exon navigation" is checked, and reload the browser window.

For more information on this feature, please consult our help page at http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html and search for "enabling item and exon navigation".

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Jonathan Casper
UCSC Genome Bioinformatics Group

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[Shawn McClelland]

Thanks!

Is there a way to automatically zoon to view the whole exon, like there is to zoom to the gene(transcript, or any feature I guess)? If so is there also a way to make a url link that will zoom to that level (I think I remember reading a way to choose the position of an entire gene, but ended up not going with it in my constructed url, but if I could do exon I think I would).

--

Shawn McClelland Ph.D.

Bioinformatics Software Developer

Thermo Scientific Genomics

Thermo Fisher Scientific

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[Jonathan Casper]

Hello Shawn,

Unfortunately there does not appear to be an easy way to link directly to a specific exon within a transcript. If you are creating these links in an automated fashion, you may be interested in obtaining the exon locations for your genes from our public MySQL server. For example, if you have a Gencode accession number, the following MySQL command will extract the chromosome, start, and stop positions of the exons for that transcript.

select exonStarts, exonEnds from hg19.wgEncodeGencodeCompV19 where name = "Your_accession_here";

The following Unix command will return that information for the transcript ENST00000456328.2.

mysql -h genome-mysql.soe.ucsc.edu -u genome -Ne 'select chrom, exonStarts, exonEnds from hg19.wgEncodeGencodeCompV19 where name = "ENST00000456328.2";'
+-------+--------------------+--------------------+
| chr1  | 11868,12612,13220, | 12227,12721,14409, |
+-------+--------------------+--------------------+

You can then use this information to build more specific URLs.

For more information about how to connect to our public MySQL server, see http://genome.ucsc.edu/goldenPath/help/mysql.html. Descriptions of the structure of individual tables on our server can be found by visiting the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTables, selecting your track and table of interest, and then clicking on "describe table schema".

The information on linking to the position of a specific gene is on our Linking FAQ at http://genome.ucsc.edu/FAQ/FAQlink.html.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

[Shawn McClelland]

Ahh, yes - actually in my object I already have that information and could quite easily generate such a link. Thanks.

I was actually asking more about if I could right click, zoom to exon, type thing. Kind of like I can right click zoom to the gene. But your idea is also doable in my workflow. Thanks

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