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  • counting tags in bam file

    Hi,

    How do i count total and unique reads (may be with 1 mm) on each chromosome from bam file ?

    Thanks,

  • #2
    for total, you can convert it to sam file using samtools, and then just do something like

    Code:
     awk '{if (substr($1,1,1)!="@") print $3}' file.sam | sort | uniq -c
    it will take a little while but it will give a nicely formatted/readable output

    for unique, it's a bit trickier, but still can be done with the same commands:

    Code:
    awk '{if (substr($1,1,1)!="@") print $3,$10}' DNT_Input.sam | sort | uniq | awk '{print $1}' | uniq -c
    Last edited by apredeus; 01-09-2013, 05:47 PM.

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    • #3
      Thanks Apredeus. can you help me understand this command ? for printing unique reads command, does it print unique reads that are perfectly matched or with mismatch ?
      Last edited by james4545; 01-10-2013, 09:20 AM.

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