I'm doing an alignment to multiple relatively short targets that are quite similar. I'm using bowtie2 for its local-alignment capabilities (and since I'm used to it).
I read the manual + some of the paper + suppl, and am still not quite sure I understand how the alignment procedure works.
I understand the reads (+its reverse-complement ) are extracted into seeds, in my case (the default) extract 20nt seeds every 10nt (my reads are paired-end <=150nt, after adapters cleaning). The seeds are than aligned and are then prioritized+combined - this last part I don't quite understand (lack of info.).
I would like to understand the following:
From seeds alignment => read alignment. What is the region of the read that is aligned? what happens if a seed is in between seeds that have a mismatch (MM).
Explanation for mismatches- by default no MM is allowed in a seed and there are overlap between seeds. my current possible explanation: at least 2 adjacent seeds are not aligned (have >0 MM) but the seeds surrounding them do align. [explanation (ignoring reverse-complement): seeds are at 1-20 seed1, 11-30 seed2, 21-40 seed3, 31-50 seed4 if seed2,seed3 are not aligned there is a gap 21-30 that can have a MM].
is there a mode where I can see the actual seeds alignments / get more in-depth explanation for each alignment.
is there a better alignment software that I can switch into easily (having SAM output and is not too slow). At this stage local-alignment is not crucial but easy from bowtie2 is.