Thread: HTseq
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Old 09-06-2012, 07:03 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
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@narges: the problem was that you sorted by coordinate rather than read name, which is required for pair-end reads.

Try instead:
Code:
samtools sort -n accepted_hits.bam accepted_hist.sorted
samtools view accepted_hits.sorted.bam | htseq-count - /hg19/Annotation/Genes/genes.gtf > count.txt
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