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,
> 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.
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