# Pre.cluster diffs option

**URL:** <https://forum.mothur.org/t/pre-cluster-diffs-option/2386>\
**Category:** Commands in mothur\
**Created:** [June 6, 2015, 2:51am UTC](https://forum.mothur.org/t/pre-cluster-diffs-option/2386 "2015-06-06T02:51:08Z")\
**Posts on this page:** 2\
**Page:** 1

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**Author:** ![waselkov](https://avatars.discourse-cdn.com/v4/letter/w/cdc98d/32.png) [@waselkov](https://forum.mothur.org/u/waselkov)\
**Post date:** [June 6, 2015, 2:51am UTC](https://forum.mothur.org/t/pre-cluster-diffs-option/2386/1 "2015-06-06T02:51:08Z")

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Hi,  
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?  
Thanks!

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**Author:** ![pschloss](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/pschloss/32/4_2.png) [@pschloss](https://forum.mothur.org/u/pschloss)\
**Post date:** [June 16, 2015, 1:20pm UTC](https://forum.mothur.org/t/pre-cluster-diffs-option/2386/2 "2015-06-16T13:20:44Z")

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What are you looking at to see that you have this difference in OTUs? Are you sure you have the files straight?