Note: People should be aware that the cow reference has changed. The old cow reference was based on Btau_4.1 (from Baylor) and the new one is based on UMD 3.1 (from UMD) so there are likely to be lots of changes. There is an updated cow assembly from Baylor (Btau_4.6) that includes the Y chromosome. UMD 3.1: http://www.ncbi.nlm.nih.gov/genome/assembly/313678/ Btau_4.6.1: http://www.ncbi.nlm.nih.gov/genome/assembly/313728/ Deanna On 3/27/12 2:22 PM, "Jennifer Jackson" <jen@bx.psu.edu> wrote:
Hi Elihu,
The latest cow genome (along with a few others) are on our active to do list and are planned to be on the public Galaxy server near term.
Meanwhile, you can obtain the genome from UCSC and use it as custom genome with TopHat. Instructions are in this wiki: http://wiki.g2.bx.psu.edu/Learn/CustomGenomes
We plan to announce the addition of new genomes via Twitter. If you don't follow Twitter, the Galaxy Update and Twitter wiki pages will also note these additions as they are included: http://wiki.g2.bx.psu.edu/GalaxyUpdates http://wiki.g2.bx.psu.edu/Galaxy%20on%20Twitter
Best,
Jen Galaxy team
On 3/27/12 3:56 AM, Aranday-Cortes, Elihu wrote:
Hi Galaxy Team,
I'd like to use Tophat but the last version of the cow genome is not listed (BotsTau7). Tha last version is listed is BosTau4 . any chance for an update?
Thanks
Elihu
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The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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