That's very helpful!  Thanks.

-Greg

On Tue, Dec 18, 2012 at 11:39 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> Hello Greg,
>
> Open up "TopHat settings to use:" to "Full Parameter list" to find the
> option: "Use Own Junctions:" and set this to "Yes". There will be a new
> option underneath it for "Use Gene Annotation Model:" - which is where the
> GTF file is entered when set to "Yes".
>
> Hopefully this helps,
>
> Jen
> Galaxy team
>
>
> On 12/18/12 8:10 AM, greg wrote:
>>
>> I'm trying to translate this command line run into the Galaxy GUI but
>> I'm not seeing a place to specify the .gtf file.
>>
>> Does anyone know?
>>
>> tophat2 -p 8 -G /groups/bowtie2_index/mRNA.gtf -o /groups/hp_1
>> /groups/genome /groups/reads.fastq
>>
>> thanks,
>>
>> Greg
>> ___________________________________________________________
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>
> --
> Jennifer Jackson
> http://galaxyproject.org
>
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