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Count difference by htseq-cout and samtools

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  • Count difference by htseq-cout and samtools

    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

  • #2
    "by bwa"? You mean "by samtools", I suppose.

    htseq-counts counts the two reads from the two ends of a paired-end fragment as one count. Samtools might count them separately, giving two counts.

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    • #3
      Yes, it should be samtools.

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