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.
You can do remove.group 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
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.
It shouldn’t meaningfully change things.
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