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  • Bowtie default parameters

    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

  • #2
    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

    Comment


    • #3
      Yeah, that's for bowtie 2. I used the original version of bowtie. I wonder if they kept the same default parameters...

      Comment


      • #4
        The default values of n and l for bowtie are different.

        See the bowtie manual

        Comment


        • #5
          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)

          Comment


          • #6
            Originally posted by GenoMax View Post
            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

            Comment

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