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  • Extract reads sequence based on position from bam file

    Dear all,
    I'm trying to recover reads sequences from specific region in bam file.
    Reads were align using bowtie2.

    I have reads align to one specific sequence and I would like to get sequences of reads mapped to a specific region of 3 nucleotides, and count the occurence of each tri-nucleotide at this position.

    How would I achieve this ?

    Thanks for your help !

  • #2
    You can extract the reads in the region you are interested in using samtools view (e.g. samtools view -b reads.bam chr1:10420000-10421000 > subset.bam) and then use bedtools/bam-readcount.
    Last edited by GenoMax; 10-10-2016, 04:53 AM.

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    • #3
      Thanks for your answer.
      Which command from bedtools ?
      What is bamcount ?

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      • #4
        Sorry. Should be bam-readcount. Added a link to post above. When you say tri-nucloetide (you want to consider the counts as a trinucleotide or just counts for bases at those three positions). If latter then bam-readcount will work.

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        • #5
          bamcount is not doing exactly what i'm asking, i don't want readcounts for each base at each position.
          I want the occurence of each tri-nucleotide at this specific site.
          For example :
          ACA = 5 reads
          GCA = 8 reads
          etc ....

          The problem is that there are INDELS in the alignment and I don't know how to deal with it.

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          • #6
            If the indel spans that position there is nothing you can do. How deep is the pileup (not practical to count in a genome viewer (e.g. IGV)?

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            • #7
              there are not that much reads mapping to the sequence of interest (maximum is 800 000 reads ).
              You are suggesting to do it with IGV ? How ?

              Comment


              • #8
                This tool by Pierre Lindenbaum may be useful in this case: https://github.com/lindenb/jvarkit/wiki/SAM4WebLogo It should give you aligned fasta files.

                If it was a small number of reads I thought you could count them in IGV but sounds like that may not be the case.

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