Hi @eaton-lab Thank you for those tips! I would like to try to keep those low represented clusters as well but my mindepth is already at 5 and my mindepth marjule at 3. Those are the minimum values right? Is there a way to go down to a mindepth value of 2? Thank you again!
@VeroIarrachtai Yes, sequences less than the value of filter_min_trim_len will be discarded. The phred offset of 33 == phred 20 is correct, so you need to add 8 to the offset to make the min phred qual = 28.