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Old 03-21-2013, 12:46 PM   #1
Location: Bethesda, MD

Join Date: Oct 2010
Posts: 47
Default HTseq-count not giving results

I am trying to use htseq-count to obtain counts per gene for my aligned files using Tophat (mm10 genome). I ran htseq on one of my samples and it seems to have worked although the counts seem to be very low overall for a 80 million read sample. I ran it a second time on another sample from the same experiment and the output file is empty. Any idea what might be wrong? my command for htseq-count is:
htseq-count -s reverse -q 21allsort.sam ./../igenome.mm10.mouse.genes.gtf > 21all.counts

I then tried a different sample in my study and still got a file of size 0. Has anyone seen this? I am not getting any errors just basically a null output.

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