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 H. Court, BVSc, PhD, Diplomate ACVA
Professor and William R. Jones Endowed Chair
Individualized Medicine Program
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