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!
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!
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