I recently started learning mothur and I am testing its functionality using an OTU dataset that I exported from Bioconductor mia (here are some examples).
I am currently looking for a function in mothur to agglomerate (sum) OTUs by a specific taxonomic rank (e.g., Family) and return the agglomerated counts table (similar to mia::agglomerateByRank). I spotted the make.shared, tax.summary and classify.otu as potential candidates, but I do not have a list file. What I have is a OTU-level count table, taxonomy, tree and sample metadata.
Could you give me a hint how agglomeration could be done in mothur?
Thanks for the question. If you have taxonomy data, you can likely reformat it into a mothur format and use our phylotype function and then go from there. The phylotypr function allows you to bin sequences at any taxonomic level. I’d suggest looking at this section of the MiSeq SOP…