new features on assembly hubs

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Michael Paulini

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Oct 10, 2016, 10:57:34 AM10/10/16
to gen...@soe.ucsc.edu
Hia,

I was just in a great presentation showing new features of the UCSC genome browser like the multi-region view and the codon count.

While the multi-region view works on track hubs, it seems not to work on my assembly hub:

Also the codon count doesn't work with BigGenePred tracks.

regards,

Michael

Christopher Lee

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Oct 10, 2016, 2:52:33 PM10/10/16
to Michael Paulini, UCSC Genome Browser Discussion List

Hi Michael,

Thank you for using the UCSC Genome Browser and your question about multi-region mode and assembly hubs, and also for your kinds words about the presentation!

Unfortunately, exon and gene-only modes are currently unsupported for assembly hubs, but you can still view multiple regions through a URL to a BED file. For more information about custom regions, please see the following page:
http://genome.ucsc.edu/goldenPath/help/multiRegionHelp.html#CustomRegions

As for codon numbering on bigGenePred tracks, be sure your trackDb.txt stanzas include the baseColorUseCds and baseColorDefault statements. Here is an example piece of a stanza with default settings:

...
...
type bigGenePred
baseColorUseCds given
baseColorDefault genomicCodons
...
...

For more information about bigGenePred fields, see the following page:
http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html#baseColorDefault

Please let us know if you have further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute


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Michael Paulini

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Oct 11, 2016, 11:34:35 AM10/11/16
to Christopher Lee, UCSC Genome Browser Discussion List
I assume I can ignore the "NOT FOR HUBS. Not yet supported " on the documentation?
Also I used itemCodons instead of genomicCodons so that the count shows up and in all cases it does not show the codons split by splice junctions (which it obviously knows about, as the count is correct and the phases of the exons too).

btw. is there any documentation on what genomicCodons, itemCodons and diffCodons actually does?

thanks,

Michael

Christopher Lee

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Oct 17, 2016, 8:13:10 PM10/17/16
to Michael Paulini, UCSC Genome Browser Discussion List

Hi Michael,

Thank you for your question about the itemCodons setting and the differences between genomicCodons, itemCodons, and diffCodons.

When you specify genomicCodons, the reference sequence is used to generate the codons. This corresponds to "genomic codons" in the drop-down. This requires CDS so it's enabled for genePred, bigGenePred, and on some PSL and bigPsl tracks (like mRNA and EST). Furthermore, if this setting is enabled, there is an option to show codon numbering, if you are zoomed in far enough (<100bp).

When itemCodons is specified, the mRNA sequence is used to generate the codons. This corresponds to "mRNA codons" in the drop-down menu for PSL tracks. mRNA sequence is not supported by bigGenePreds, and we are unclear as to how your hub is able to function with that setting. Additionally, the codon numbering setting is not available when using itemCodons.

When diffCodons is specified, the only codons that are drawn are ones where the mRNA codon is different from the reference codon. This corresponds to "non-synonymous mRNA codons" in the PSL track drop down, which again needs mRNA sequence to work, and again does not have codon numbering available.

Thus "genomicCodons" should be the correct setting for your hub.

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

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