Bowtie 2 parameters, how does this make sense

[KnowNothing2]

When I run:

--very-fast-local -L 20 -N 1

I get ~70% coverage onto my genome

To make my conditions less stringent, I ran

-D 5 -R 1 -N 1 -L 15 -i S,1,2.00 (which is essentially very-fast-local with a seed length of 15 and a mismatch of 1)

However, I get 0.02% coverage onto the same genome from the same file as used above.

What is going on?

[dpryan]

Presumably -L 15 is causing so many false matches that bowtie2 gives up. That's why the presets have increasing seed-length with decreasing -D.

[KnowNothing2]

Presumably -L 15 is causing so many false matches that bowtie2 gives up. That's why the presets have increasing seed-length with decreasing -D.

Makes sense; however, if I recall correctly I ran --sensitive-local a few days ago and I got a lower coverage than with --very-fast-local.

[dpryan]

I can conceive of a number of possible reasons, but it's tough to know which is correct without seeing the reads and the genome.