BFAST average mismatch quality?

[genlyai]

Hi everyone,

I'm starting to use BFAST after having used only Bowtie till now (and holy crap it aligns a lot more reads).

Anyway, I wonder if anyone can explain what the -q (average mismatch quality) option does and how it affects the results. Maybe I'm skimming too fast, but I'm not finding an explanation in either the manual or in the BFAST paper.

Thanks for any help!

[nilshomer]

It mainly affects the mapping quality, essentially acting as a scaling factor. The default value works well, though you are free as always to play around with it.

[genlyai]

Thanks Nils.

In that case, it seems safe for me to ignore, as long as it doesn't affect the alignments reported with my relaxed settings.

Again, great program.