Hello Sheena,

If you concern with using the UCSC version of the database has to do with the chromosome naming and downstream Cufflinks analysis using Ensembl's reference GTF files, please see #5 on our FAQ, which demonstrates how to modify an Ensembl GTF file to be compatible with the UCSC chromosome naming (slight changes may be needed for each particular genome):
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq

If there is another reason, please know that custom reference genomes (in fasta format) can be uploaded using FTP following this method: http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

Hopefully this helps,

Best,

Jen
Galaxy team

On 11/4/11 2:50 PM, Scroggins, Sheena wrote:
How do I upload the Zebrafish genome from Ensembl to my user history in
Galaxy? I’m trying to map my RNA-Seq data using TopHat and need to map
it to the Ensembl version of ZFv9, but Galaxy only has the UCSC version
built in. The Ensembl version is slightly different.
Thanks,
Sheena


___________________________________________________________
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:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
___________________________________________________________
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:

 http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

 http://lists.bx.psu.edu/

Reply via email to