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  • mendl7
    replied
    Excellent. Thanks for pointing out the sources they are in. Cheers.

    Leave a comment:


  • nilshomer
    replied
    Originally posted by mendl7 View Post
    Does anyone know of a good source for understanding the alignment description format of Bowtie's MD tag? I'm trying to work out a parser to give me a simple alignment of reference/read from this information. Thanks!
    You can take a look at the source code within SAMtools for creating the MD tag (bam_md.c) or within the PERL SAM module (http://search.cpan.org/~lds/Bio-SamT.../Bio/DB/Sam.pm). Both will show you how to recover the reference sequence using the MD tag and the cigar.

    Leave a comment:


  • mendl7
    started a topic Bowtie MD tag format reference

    Bowtie MD tag format reference

    Does anyone know of a good source for understanding the alignment description format of Bowtie's MD tag? I'm trying to work out a parser to give me a simple alignment of reference/read from this information. Thanks!

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