Entering edit mode
7.6 years ago
ariel.balter
▴
260
I'm doing chipseq analysis, so using aln
vs mem
because of short reads. A pipeline I'm basing mine off of calls bwa aln
with -q 5
. The docs say:
-q INT Parameter for read trimming. BWA trims a read down to argmax_x{\sum_{i=x+1}^l(INT-q_i)} if q_l<INT where l is the original read length. [0]
That equation is essentially
Where qi<q for all i.
However, this does not define either x or the values of the qi
I'm happy to go into the math, but if someone could just explain how I would use this parameter in practical terms, that would be totally sufficient.