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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.Originally posted by mendl7 View PostLeave a comment:
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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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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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