That's very helpful! Thanks. -Greg On Tue, Dec 18, 2012 at 11:39 AM, Jennifer Jackson <jen@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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
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