Why does `bowtie` only find perfect matches even when specifying mismatches? (ie. `-n 3`)

Question

[giova34]

I tried a few methods to align a set of 32-mers against a reference genome, to find where they may potentially align with at most 3 mismatches.

bowtie --sam -v 3 -p 8 --all -f --norc hg38 kmers.fa kmers_aln.sam

When using bowtie, even though I specify the number of mismatches -v 3 and to capture all possible alignments -a, the resultant matches are all perfect matches (CIGAR = 32M). Is there a different parameter I am missing that increases the aligner's sensitivity? Additionally, for personal learning, why isn't bowtie able to capture the mismatches - is it because it only ranks its matches and saves only the exact matches?

Answer 1

[swbarnes2]

You can't tell the number of mismatches from the CIGAR. Just insertions, deletions, clippings, etc.