Hi,
I used bowtie to align a set of pair-end reads to the reference sequence and I used two programs to count the reads:
1) samtools - "samtools view -c -q1 my.sorted.bam chr_ID"
2) htseq-count - "htseq-count -s no -t CDS -a 1 my.sorted.sam my.gff"
One interesting thing about these counts is that the counts by bwa is exactly twice of those by htseq. Can anybody help explain?
Thank you,
Douglas
I used bowtie to align a set of pair-end reads to the reference sequence and I used two programs to count the reads:
1) samtools - "samtools view -c -q1 my.sorted.bam chr_ID"
2) htseq-count - "htseq-count -s no -t CDS -a 1 my.sorted.sam my.gff"
One interesting thing about these counts is that the counts by bwa is exactly twice of those by htseq. Can anybody help explain?
Thank you,
Douglas
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