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  • Bismark Alignemt (Cytosine coverage)

    is there any way to check the coverage of a particular nucleotide (say C) in aligned region (Bismark Alignment) compared to the total C in the genome. i.i how much of the total 'C' are covered in our aligned region?

  • #2
    I guess you could filter the BAM file for your region of interest (using samtools), and then use the metyhlation extractor and bismark2bedgraph on the file. A simple line count in the resulting coverage file will give you the number of Cs covered.

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