Thanks for your replies!
But I still have something confused. The pair-end reads were processed using
qiime dada2 denoise-paired to get
rep-seqs.qza. Then the
rep-seqs.qza were use to get OTUs using
qiime vsearch cluster-features-de-novo. And you also think it is feasible.
However, when I looked back on this section OTU Clustering, I found four requirements on sequences, one of which is
reads are all trimmed to the same length. As far as I can see, the lengths of the sequences in
rep-seqs.qza, which is from DADA2, are not the same, so the differences in the sequence lengths will have negative effects on clustering results?
By the way, in this link removing-non-biological-sequences, I think the sentence
If you’re going to use DADA2 to denoise your sequences, you can remove **biological** sequences at the same time as you call the denoising function. should be revised to
If you’re going to use DADA2 to denoise your sequences, you can remove **non-biological** sequences at the same time as you call the denoising function.