What Version Of Ensembl Is Ucsc Genome Browser Using?
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11.0 years ago
user ▴ 940

how can one find out what version of Ensembl UCSC is using when you download the ensGene table from UCSC? Is it guaranteed to be the same for each genome? For example once a new genome, say hg19, is released, does it use a fixed version of Ensembl and stick with it even with new Ensembl releases (based on hg19) are made? thanks.

ucsc genome-browser annotation ensembl • 3.4k views
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11.0 years ago
Neilfws 49k

Your question is answered at the UCSC mailing list.

The human ensGene track is currently labelled Ensembl 71, i.e. it is the latest version (edit: almost the latest version; see comments).

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We're currently on Ensembl 72, so that's not the latest version. To get the latest Ensembl data, I would recommend getting it from Ensembl.

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I stand corrected. "Data last updated: 2013-05-02", so I guess version 72 is pretty recent and UCSC will update soon.

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that's helpful but how do you get it programmatically from goldenPath ftp? if you download http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz for example on a given date how do you find its associated Ensembl version? I don't want to go through the tables interface with the browser

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Well, since version is not recorded in any of the ensGene-related files at the FTP site, the answer is that you cannot get it programmatically. Best you can do is use "wget --timestamping" so as to at least know when the file was updated, then I guess compare that date somehow with dates of Ensembl releases.

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