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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