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  • Counting Reads in BAM file per genomic position

    Hello,

    I am looking for a tool or script that counts the number of reads in a bam file by position, and takes into account only successfully paired reads. I would like to estimate PCR duplicates when making the (possibly erroneous, I understand!) assumption that reads with the same genomic coordinates are copies.

    For example, for the following input:

    Chr1:1-500
    R1--------------> <---------------R2
    R1--------------> <---------------R2
    R1--------------> <---------------R2

    Chr1:5-505
    R1--------------> <---------------R2

    Chr1:10-510
    R1--------------> <-----------R2
    R1--------------> <-----------R2
    R1-------------->

    I would like to output this information:
    Chr1:1-500 3
    Chr1:5-505 1
    Chr1:10-510 2
    Last edited by C9r1y; 11-24-2015, 02:31 PM.

  • #2
    bedtools multicov with the argument -p.

    Comment


    • #3
      Thanks blancha for the response. However, I would like the position coordinates to be dictated by the read positions, not a bed file of genomic regions.

      I would like to estimate the number of pcr duplicates, and will make the assumption that reads that have the exact same start and stop sites are duplicates,

      Comment


      • #4
        Then use SAMtools rmdup or Picard MarkDuplicates, since those tools identify duplicates by the same criteria you're using.

        Comment


        • #5
          Sorry, tired.
          How about this one? From Stanford.



          It has an option -counts.

          Otherwise, you may just have to find someone to write you a custom script.
          I don't know of any tool to give you exactly what you want, although it may exist.

          Comment

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