Remove group after OTU clustering?

I finish the analysis of a group of samples. After looking at the results, I would like to remove one group and exclude it from the analysis.
Should I remove the group and dist and cluster again and then make.shared and classify.otu again?
Will the OTUs change if one sample is removed or is it possible to make the shared file excluding one group using the same dist and cluster outputs? It’d be good to avoid repeating dist and cluster as those take a lot of time and memory but I don’t want to make a mistake.
Thank you!


You can do whenever you want. In the SOP we do it before clustering, but you can also do it after make.shared or as soon as you create a group file with make.contigs.


Hi Pat

I thought that if I removed a group and its corresponding sequences, I should cluster again at 97% id because sequences that were included in one OTU now might be included in another one, changing the OTU abundances result.

Thank you


It shouldn’t meaningfully change things.

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