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 q_i<q for all i.

However, this does not define either x or the values of the q_i

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.