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
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