bowtie2 filter for maximum alignment score

Question

[rishi]

Is it possible to set a filter/argument in which bowtie2 reports just one alignment for each seed, the one which is of the highest alignment score and not the mapping quality? I'm confused with the default mode options.

[Brian Bushnell]

I don't understand your question; I generally think of alignment score and mapping quality as synonymous. Can you clarify what you are trying to do?

[rishi]

I think MAPQ is the number of times the seed is aligning to the genome, and score is the alignment score after bonuses and penalties for each seed (I may be wrong). When I put D as 20 (say), bowtie2 tries to align the seed 20 times and reports all the alignments above a particular maximum alignment score. The manual says "It will eventually stop looking, either because it exceeded a limit placed on search effort (see -D and -R) or because it already knows all it needs to know to report an alignment. Information from the best alignments are used to estimate mapping quality (the MAPQ SAM field) and to set SAM optional fields, such as AS:i and XS:i. Bowtie 2 does not guarantee that the alignment reported is the best possible in terms of alignment score". Is it somehow possible to not make my seeds align multiple times, and instead instruct bowtie2 to choose the correct one?

Answer 1

[Devon Ryan]

Bowtie2 already reports the single best alignment of all seeds that it uses. That is the default. The alignment with the highest score will always have the highest MAPQ, since all other alignments would have a MAPQ of 0 or 1 (the bowtie2 algorithm for this is a bit odd, don't ask).