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.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>
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