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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