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dpryan · 09-06-2012, 07:03 AM

@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

09-06-2012, 07:03 AM	#4
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	@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