Cluster command is giving me a large number OTUs, more than it should be

Hello there,
While runing Mothur commads, there is a result that does not fit, and it is the high number of OTUs that we are getting in the cluster command. We know that it is impossible to have more than 10000 OTUs in our type of samples and we think there is a problem with the alignment, or even before, at the time of making the contigs, that then generates this great diversity. I should get about 2000-3000 OTUs and I get five times more.
Someone please help me in solving this issue?
Thanks you all.


Can you tell us more about what you’re sequencing and what region you’re looking at? What sequencing platform?


Thanks you so much for responding so fast :slight_smile:
We’ve sequenced 16S rRNA using 515f and 806r primers and MiSeq Illumina sequencing platform.

I suspect you’re running into problems with sequencing error since the region is longer than will allow you to get two fully overlapping reads of 250 nt. You might want to check out this post… Why do I have such a large distance matrix


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