I’m wondering about the results I get when I change the “diffs” option in the pre.cluster command. As far as I understand, diffs=1 (the default) merges sequences that are within 1 mismatch of each other, whereas if I change it to diffs=2, this merges sequences within 2 mismatches of each other. So why do I end up with around 500 OTUs when diffs=1, and over 2000 OTUs when diffs=2 (all other conditions being equal) for the same dataset? Wouldn’t you expect more OTUs when the mismatch value is lower, since fewer sequences are being lumped together? Am I missing something obvious?
What are you looking at to see that you have this difference in OTUs? Are you sure you have the files straight?