Hi Zain, Annotations are used with Tophat2 the same way that they are with Tophat. Open up the full parameters on the tool form and change the option "Use Own Junctions:" to "Yes". Here you can now supply gene models as set related parameters. If actually performing this operation is problematic and producing errors, please submit a bug report, leaving inputs and outputs undeleted, so that we can troubleshoot. The wrapper is still somewhat new. Hopefully this helps & have a nice weekend, Jen Galaxy Team Jennifer Hillman-Jackson http://galaxyproject.org

On Nov 1, 2013, at 3:22 PM, Zain A Alvi <zain.alvi@student.shu.edu> wrote:

Hi Jenn,

I hope this reaches you well. I was trying to use tophat 2 on the public Pennsylvania Galaxy server and noticed that I was not able to supply the GTF file. Although it lists that providing GTF file is an option on the bottom of the tophat 2. I was wondering if it possible to add the option to provide an GTF file for Galaxy's Tophat 2. I have attached a screen shot for your kind review as well.

I would really appreciate it if it was possible.

-G/--GTF [GTF 2.2 file] Supply TopHat with a list of gene model annotations. TopHat will use the exon records in this file to build a set of known splice junctions for each gene, and will attempt to align reads to these junctions even if they would not normally be covered by the initial mapping.

Sincerely.

Zain <Galaxy_Tophat2_GTF.jpg>