bowtie adjust alignment options

[antoza]

Hi everyone,

I am also new. I have started to work as a PostDoc in a mutant resequencing project and i am using bowtie for mapping paired end reads against a reference assembly. I would be grateful if someone knows how exactly can i refine aligment options in bowtie in aspects of lenght of match (40%) and similarity levels (70%) for each read in order to relax mapping stringency. I am trying to figure out this and i think is probably something with -n/--seedmms and -e/--maqerr but i am not quite sure.
Any help would be so helpful.
Antonio

[mastal]

I am not very familiar with Bowtie2, but in Bowtie1 the parameters to change would be -n or -v, and -l.

[dpryan]

In bowtie2, the parameters you might want to look at are:

• -N number of seed mismatches, default is 0, but this can also be 1, though that will significantly slow things down
• -L seed length, make it shorter if you want to increase sensitivity (see also the presets)
• --score-min This effectively sets the minimum alignment score to declare an alignment valid. It's length dependent and the defaults change according to whether you use local or end-to-end alignment. In general, if you relax the --score-min function, you'll get more alignments with greater mismatches. Keep in mind that bowtie2's MAPQ calculation function depends heavily on this (the lower the minimum score is, the higher the MAPQ will be for a given read with a given number of mismatches).
• -D Number of failing seed extensions, see also the presets
• -R Number of repeat seeds, see also the presets