This section covers the use of RDP’s web-based tools for processing sequences to the point of having files you can import into R and use for community analyses. There are two general paths: “supervised” and “unsupervised.” With the supervised method all sequences are classified with the RDP classifier resulting in a file giving counts for taxa by samples and the taxonomies of the taxa. This file can be imported into phyloseq to fill the otu_table and tax_table slots. With the unsupervised method, sequences are clustered based on similarity, with each cluster representing an operational taxonomic unit or OTU. The OTUs can then be classified and representative sequence for each obtained. Thus this method supplies files to fill OTU_table, tax_table and rep_seq slots in an experiment level phyloseq object.
The initial processing step is the same for both methods.