Hi Michael, Thanks for reporting this, sounds like an older, incorrect, config file is in place. And this can be fixed. I will be going into the genomes area and re-verifying current builds and other built-in data/indexes shortly. Thanks! Jen Galaxy team On 10/10/13 1:56 PM, Court, Michael wrote:

Hi,

I minor annoyance that I had found with the current implementation of "Tophat for Illumina (version 1.5.0)" in the public usegalaxy.org site:

When you submit sequences for alignment, the dropdown list of available genomes gives 2 dog genome choices -- BUT both are labeled the same -- "Dog(Canis lupus familiaris): canFam2".

After trial and error I found that the second (lower on the list) choice is actually "Dog(Canis lupus familiaris): canFam3.1".

Hopefully this can be corrected at some point -- maybe when the next release comes out from the Broad.

Michael

*Michael H. Court, BVSc, PhD, Diplomate ACVA*

*Professor and William R. Jones Endowed Chair*

*Individualized Medicine Program*

*Pharmacogenomics Laboratory*

*Department of Veterinary Clinical Sciences*

*College of Veterinary Medicine, Washington State University*

*100 Grimes Way, Pullman, WA 99164-6610***

*Office: 509-335-0817 Cell: 774-287-7082 Fax: 509-335-0880*

michael.court@vetmed.wsu.edu <mailto:michael.court@vetmed.wsu.edu> www.vetmed.wsu.edu <http://www.vetmed.wsu.edu/>**

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