I have just performed the dada2 denoising step. I have a rep seqs file and a feature table file. Should I move on to perform OTU clustering right now? On the clustering seqs plugin page it says that I need to perform sequence dereplication. Do I need to do that?
The answer to your question really depends on what the goal of your analysis is. You can technically use the feature table and rep-seqs you have obtained from DADA2 to all your downstream analysis. The benefit of using this method is that you retain the highest accuracy of the sequences all the way through your analysis and is the recommended method unless you have a very specific reason to do OTU clustering. For example you might use OTU clustering for benchmarking, comparing to previous studies, or using some custom tool/dataset that requires OTUs. If you’re still not sure, let us know what exactly you are trying to get out of your analysis and we can offer more help!
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.