Bowtie default parameters

[ThePresident]

Hello,

I have a very simple question about bowtie:

If I run bowtie without explicitly specifying the mode, the default mode should be used (which is -n mode), right? Now, if I don't specify neither the number of mismatches (-N) nor seed length (-L), what are the default parameters for N and L then?

Thank you in advance,

TP

[GenoMax]

For bowtie2

-N <int> max # mismatches in seed alignment; can be 0 or 1 (0)
-L <int> length of seed substrings; must be >3, <32 (22)

N = 0 and L = 22.

Presets: Same as:
For --end-to-end:
--very-fast -D 5 -R 1 -N 0 -L 22 -i S,0,2.50
--fast -D 10 -R 2 -N 0 -L 22 -i S,0,2.50
--sensitive -D 15 -R 2 -N 0 -L 22 -i S,1,1.15 (default)
--very-sensitive -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

For --local:
--very-fast-local -D 5 -R 1 -N 0 -L 25 -i S,1,2.00
--fast-local -D 10 -R 2 -N 0 -L 22 -i S,1,1.75
--sensitive-local -D 15 -R 2 -N 0 -L 20 -i S,1,0.75 (default)
--very-sensitive-local -D 20 -R 3 -N 0 -L 20 -i S,1,0.50

[ThePresident]

Yeah, that's for bowtie 2. I used the original version of bowtie. I wonder if they kept the same default parameters...

[mastal]

The default values of n and l for bowtie are different.

See the bowtie manual

http://bowtie-bio.sourceforge.net/manual.shtml#the--n-alignment-mode

[GenoMax]

N and L are not valid options for bowtie 1.0 (but n and l are)

-n/--seedmms <int> max mismatches in seed (can be 0-3, default: -n 2)
-e/--maqerr <int> max sum of mismatch quals across alignment for -n (def: 70)
-l/--seedlen <int> seed length for -n (default: 28)

[ThePresident]

N and L are not valid options for bowtie 1.0 (but n and l are)

Darn, I was looking at wrong place... Anyway, thanks alot!

TP