I have a few questions regarding taxonomy analyzing with the Phyloseq R package:
As mentioned in the phyloseq tutorial, it needs three files:
OTU Taxonomy Samples
Question1: should I separate my otu table obtained from Qiime2 in two tables? one for taxonomy table and another one for otus counts- in two different excel files.
Question2:Is the sample file equal to metadata file? Or what?
Please clarify the questions above.