Which table (after denoiseing or clustering) is better to be used to create otu table?

[kaile]

There are two ways to create otu table-using the table after “denoise-singe” or “vsearch cluster-features-de-novo” function. I am confusing which way is better to be applied to further analysis. Does anyone have good suggestions?

[ebolyen (Evan Bolyen)]

Hi @kaile!

There are good reasons to cluster your data after denoising and good reasons to leave it alone. I think you would be interested in this recent topic, which covers a lot of ground related to your question:

To cluster or not to cluster?

Hello - I would like to bring up a topic that has been discussed before (A quick clarification on clustering) and provide an example from my own analysis. I am looking at one particular taxonomic group within environmental samples of bacterial populations. The method of denoising is dada2, so I am assuming that OTU clustering was not necessary since sequencing errors are accounted for during the denoising process. However, this analysis resulted in many OTU's being defined, some of them quite r…

[kaile]

Thanks so much for your clear clarification!