Pre.cluster parameter diff tuning

Commands in mothur
1

Hi all,

I’m using default diff=2 for pre.cluster command. However, there are only a small reduction in number of unique reads (2.2 million to 2 million). Since there are so many unique reads, should I set a larger diffs, e.g., diffs =2 or diffs = 5 to reduce the number of unique reads. My data is from V3 region and I’ve customized alignment of silva to V3 region.

Thanks,
Ray

2

The rule of thumb that I recommend is 1 diff per 100 nt of sequence data. If you are sequencing the V3 region, that is ~195 nt (Customize your reference alignment for your favorite region). So I would not use more than diffs=2

Pat

3

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