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Question: How To Provide .Gtf File To Tophat2
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6.0 years ago by
mailing list • 840
mailing list • 840 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
alignment bowtie • 1.1k views
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modified 6.0 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.0 years ago by mailing list • 840
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6.0 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 -- Jennifer Jackson http://galaxyproject.org
ADD COMMENT • link written 6.0 years ago by Jennifer Hillman Jackson ♦ 25k
That's very helpful! Thanks. -Greg
ADD REPLY • link written 6.0 years ago by mailing list • 840
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