we have followed the Schloss SOP but with our own dataset (16S rRNA analysis (v3-v4 region) of two samples from two different saline habitats).
At the moment we are at the step “Preparing for Analysis” and have created the OTUs by the command “cluster.split” and assigned taxas to the OTUs by classify.otu. We have derived a huge amount of OTUs comprising only one representative sequence (75% of the total number of generated OTUs). Our assumption would be that this is affected by sequencing errors, at least partially. And hence the diversity is inflated. Unfortunately, we don’t have a sequenced mock community, yet.
Without being too bold would it be possible to hint us to one of the conducted commands and their parameters so we end up with less OTUs filled with just one sequence. As we guess we have to alter one of the “filters” at the command unique.seqs.
As always we are grateful for any advice or hint!