Is this removing PCR duplicates or removing TRs and reads for best-best-best.
A bug I found is that pcr duplicates (which we do not have) are being removed, some 20k read trs. Step 15 finds duplicates and doesn't remove them, but then step 16 is removing them though I said: KEEPPCRDUPS=1 . I don't know how to fix that.
Executing step #16 (removing mapped duplicates) ...
79204 entries deleted!
39602 reads deleted!
Is this removing PCR duplicates or removing TRs and reads for best-best-best.
A bug I found is that pcr duplicates (which we do not have) are being removed, some 20k read trs. Step 15 finds duplicates and doesn't remove them, but then step 16 is removing them though I said: KEEPPCRDUPS=1 . I don't know how to fix that.
Executing step #16 (removing mapped duplicates) ...
79204 entries deleted!
39602 reads deleted!