I'm struggling with the fact that I want to align thousands of ~4KB PacBio sequences to short primer sequences (~20B). (Just seeying which sequences contain the primer sequence). I've tried bowtie2 and blasr so far but both come up with empty results. Trying to change parameters influencing this resulted in nothing so far... so thats why I need your help ;) Anyone knows what parameters to use for this case?
Parameters I used now:
bowtie2 -f -S --local -N 1 -L 10 --no-sq --no-unal -p 12 -x <Index> -U <PacBio>
blasr <PacBio> <Reference> -noSplitSubreads -sam -minPctIdentity 90 -minMatch 10 -nproc 6