no. of alignments in bowtie2

[tirosho]

does bowtie2 have a default for number of alignments (-k parameter)?

if so what is it? if not, how many alignments does it search for if i don't specify any k.

my problem is basically that I'm aligning my reads through a database and there is a significant portion which is not aligned although it should be.
Thanks for all help!

[dcameron]

The default settings for bowtie2 (bowtie2 --help) are:

Reporting:
  (default)          look for multiple alignments, report best, with MAPQ

And the parameters that determine how thoroughly it searches are:

 Effort:
  -D <int>           give up extending after <int> failed extends in a row (15)
  -R <int>           for reads w/ repetitive seeds, try <int> sets of seeds (2)

Unfortunately, that doesn't give the maximum attempted locations, merely the maximums for badly chosen seeds. I suspect it depends on how many close hits there actually are.