Daniel:Notebook/GenomeMiner/2013-8-7

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Revision as of 22:26, 7 August 2013 by >Djacobse
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HL155

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Continuing the analysis of the HL155 data. I looked through the information on the bowtie2 manual. The 12th column of a SAM output contains several possibly useful pieces of information:

From Bowtie2 manual

XM:i:<N> The number of mismatches in the alignment. Only present if SAM record is for an aligned read.
NM:i:<N> The edit distance; that is, the minimal number of one-nucleotide edits (substitutions, insertions
and deletions) needed to transform the read string into the reference string. Only present if SAM record is for
 an aligned read.