Daniel:Notebook/GenomeMiner/2013-8-7
Jump to navigation
Jump to search
HL155
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.