bowtie 2 mismatch parameters for interspecific alignments?

Question

[roberthbbaird]

Hi all,

I am using Bowtie 2 for an interspecific alignment (specifically between two fungus gnat/Sciarid species). I am mapping pair-end Illumina reads to an Illumina genome assembly.

The default maximum and minimum mismatch penalties are 2 and 6, but I am aware that I may need to change these given that I am doing an interspecific alignment. However I've never used Bowtie before and have no idea what to change them to. Does anyone have experience using Bowtie 2 for interspecific alignments and could recommend which maximum and minimum mismatch penalties to use?

Thanks in advance.

[GenoMax]

Try doing the alignment with defaults first. Even if you are doing the alignments across species the sequence is not going to have have that many differences in each read.

Consider looking at BBMap (a guide is here) as an alternate aligner. You have multiple options you can change/consider.

Answer 1

[Istvan Albert]

I would recommend running the aligner with one of the presets, for example --very-sensitive-local the bowtie2 help will explain what this label corresponds to

  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