I am aligning paired-end ChIP-Seq data of drosophila transcription factors.
I would like to have a .sam file with the following alignments reported: - A maximum of three mismatches, i.e. three wrong bases (this is the option --max-mismatch=3) - But, if there are possible alignments with only one mismatch, and also possible alignments with two mismatches, I want only the alignments with one mismatch reported.
I thought -M 0 (same as --suboptimal-levels=0) would be my option, but it doesn't work. I think it works on the mapping quality field (i.e. MAPQ).
The --npaths=1 option doesn't do it for me as well, because it reports only one (the best) alignment, even if there are multiple possible alignments with the minimum number of mismatches.
I hope I stated my aim clearly. Does anyone know how I could obtain this specific subset of alignments? I fear I might have to resort to Python and code it up by myself, but want to make sure there is no easy solution available first.