After Clustering ASVs of DADA2, what exactly to deal with the New OTU table?

[fenglong616]

Hi, I am new about metadata, I am trying to follow the pipe ITS of Dada2, and I got the ASVs table, but I want to cluster the ASVs to an OTUs table.(97%) according to the codes you have been given, I have OTUs table now. But I am wondering about what to do next. I am going to use Phyloseq for processing. I am not sure about the ASVs_ taxonomy can be used for the OTUs table.
Do I need to assign taxonomy by the new OTU? and how can I do it? I am so confused about the process.

[benjjneb]

If your OTUs have a representative sequence associate with them, you can run assignTaxonomy on those sequences. Otherwise, I'd look towards whatever software you used to make OTUs for guidance on how to assign taxonomy to them.

[fenglong616]

@benjjneb Hi again, thanks for your reply! I tried to do assign taxonomy, it seems like does not work! I upload the screenshot of my script. it is based on the tutorial of DADA2, I am not sure whether it is correct after clustering ASVs to the new OTUs. could you give me more advice?

[benjjneb]

You want to make sure that whatever you give assignTaxonomy (in this case merged_seqtab) can correctly get the DNA sequences in character format extracted from it by the dada2::getSequences function.

The easiest thing is to just make a character vector yourself to ensure its in the right format. That is, extract a character vector of the cluster sequences from the merged_seqtab object, and give that to assignTaxonomy.