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  • samtools mpileup and overlapping paired-end reads

    I am using samtools mpileup to generate a pileup for paired-end RNA sequencing data. I am curious about how samtools handles pair mates whose read mappings overlap. With regard to the simple example below, for positions 7-11, are both pair mates enumerated?

    Code:
    position     1    6    11   16
    reference    ATGCATGCATGCATGC
    pair mate 1  ATGCATGCATG
    pair mate 2'       GCATGCATGC    (reverse complemented)
    I am parsing the pileup output to quantify RNA editing at some positions and do not want to count an 'RNA molecule' twice just because the read pair mates 'overlapped.'

    Thanks.

  • #2
    cross posted on http://www.biostars.org/p/87299

    Comment


    • #3
      Originally posted by lindenb View Post
      Sorry, is cross-posting a no-no? I am trying to reach more people and plan to post here a link to any conclusive answer I get elsewhere.

      Comment


      • #4
        Originally posted by alpha2zee View Post
        I am using samtools mpileup to generate a pileup for paired-end RNA sequencing data. I am curious about how samtools handles pair mates whose read mappings overlap. With regard to the simple example below, for positions 7-11, are both pair mates enumerated?
        Hi- I'm pretty sure mpileup is going to double count overlapping reads. You can clip overlapping mates with, among other tools, clipOverlap .

        Dario

        Comment


        • #5
          Originally posted by alpha2zee View Post
          Sorry, is cross-posting a no-no? I am trying to reach more people and plan to post here a link to any conclusive answer I get elsewhere.
          It's frowned on because it's a waste of time for someone here to compose a good answer for you, when they don't know that you already have a good answer somewhere else.

          I think it would have been better to have posted on one site, and if after a couple of days, you got no good answer, then posted the question somewhere else.

          Comment


          • #6
            Originally posted by dariober View Post
            Hi- I'm pretty sure mpileup is going to double count overlapping reads. You can clip overlapping mates with, among other tools, clipOverlap .

            Dario
            Thanks. I got the same answer on my cross-post on biostars.org. And thanks for suggesting clipOverlap.

            Comment


            • #7
              Note, the above answer is now incorrect, if you're using samtools >= 1.0 (which was released more than 3 years ago).

              See my post here: https://www.biostars.org/p/87299/#284421

              Comment

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