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" <j...@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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___________________________________________________________
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