BWA, I don't know what I'm doing

[asheenlevrai]

Hello,

I'm not really sure I understand how to setup parameters in BWA.

I want to map 25bp non-paired reads to the mouse genome. I try to do that on galaxy...

I made an alignment using the following parameters:
- max edit distance (aln-n) : 0
- fraction on missing alignments given 2% uniform base error rate (aln-n) : 0.04
- max gap open (aln -o) : 1
(I wanted to allow 1 gap)

- max gap extension (aln -e) : -1
- disallow long del within (val)bp towards 3' end (aln -d) : 30
- disallow in/del within (val)bp towards the end (aln -i) : 30
(I guess that screws up my will to allow 1 gap since the reads are 25bp long and gaps are insertions, right?)

- # of 1st subsequences to take as seed (aln -l) : 30
- max edit distance in the seed (aln -k) : 2
- missmatch penalty (aln -M) : 3
- gap open penalty (aln -O) : 11
- gap extension penalty (aln -E) : 4
- max # of alignments to output in the XA tag (samse -n) : 3

I guess this settings should allow 0 gaps and 0 missmatches (MM), right?
However, I end up with an alignment where many reads have 1 or 2 MM.
Did I miss something?

what setting should I use to allow for 1 gap and 3 MM?

Thank you very much in advance for your help.
-J-