I have NextSeq 1x75 bp sequencing data that I'm trying to align using relaxed settings. My goal is to allow alignments with up to 4% mismatches. To do this, I have come up with the following command in bowtie:
bowtie -S -p 16 -n 3 -l 75 ref reads.fastq out.sam
With these settings I believe that I am allowing for 3 mismatches per 75 bp, or per read, resulting in up to 4% mismatches. Is what I believe is happening congruent with what is actually happening?