Hello,
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.
Thanks.
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.
Thanks.
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