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Old 05-17-2015, 02:19 AM   #3
Location: London

Join Date: Jan 2015
Posts: 10

But, for example, say I downloaded the hg19 version at the iGenomes page.. in the file I find the chr10.fa reference file, which I create the bowtie index (bt2 files).. then theres also a GTF file for the whole genome..
so is it correct if i run tophat like this:
tophat -p 8 -G hg19.gtf chr10 reads1.fastq,reads2.fastq

Everytime I put the GTF file it simply won't work.. I also tried assempling transcripts with cufflinks using a bam file generated on tophat without the GTF file (only the chr10 bowtie index reference)..

The thing is: do I need to manipulate these files before putting them for a run?

I am sorry! I am verry new to this and tried several times changing small things in these files but simply didn't work.
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