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 

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,

Galaxy Team

Jennifer Hillman-Jackson

> On Nov 1, 2013, at 3:22 PM, Zain A Alvi <zain.a...@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>
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:


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


To search Galaxy mailing lists use the unified search at:


Reply via email to