[galaxy-user] How to Provide .gtf file to tophat2

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

Re: [galaxy-user] How to Provide .gtf file to tophat2

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