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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