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Old 01-21-2014, 07:13 PM   #1
witty
Junior Member
 
Location: RI

Join Date: Nov 2013
Posts: 5
Default GTF file for read counts

Hi,

I try to get the read counts for gene differential expression analysis using the following command:

htseq-count -m intersection-strict –stranded=no testsort.sam gene.gtf > testsort.counts

Can you tell me what kind of "gene.gtf' file I should use? I used ABySS(de novo assembly) for my transcriptome assembly so it seems I haven't the available reference genome.

I appreciate your help!
Victoria
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