Daniel:Notebook/GenomeMiner/2013-8-7: Difference between revisions
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Continuing the analysis of the HL155 data. I looked through the information on the [http://computing.bio.cam.ac.uk/local/doc/bowtie2.html bowtie2 manual]. | Continuing the analysis of the HL155 data. I looked through the information on the [http://computing.bio.cam.ac.uk/local/doc/bowtie2.html 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. |
Revision as of 22:26, 7 August 2013
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.