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

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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.