Hi!
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 in advance!