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Old 03-25-2013, 04:48 PM   #6
joseph.troy
Junior Member
 
Location: Urbana, IL

Join Date: Oct 2012
Posts: 4
Default Question about removing the GTF file

Thanks all for the information! I'm having the same problem. I tried removing the GTF file, but perhaps did it wrong (see with and without below). If possible can you share your command lines without the GTF file?

My command with GTF file...
tophat -p 8 -o tophat.out --library-type fr-firststrand -G ~/jmt/projects/run3_01/mm9gtf/genes.gtf --transcriptome-index ~/jmt/projects/run3_01/mm9transcripts/transcriptome ~/jmt/projects/run3_01/mm9genome/genome test.fastq


My command without the GTF file...
tophat -p 8 -o tophat.out --library-type fr-firststrand --transcriptome-index ~/jmt/projects/run3_01/mm9transcripts/transcriptome ~/jmt/projects/run3_01/mm9genome/genome test.fastq

-Thank you!!
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