I have a question regarding the get.oturep command. My goal is to generate a file that contains a sequence for each OTU, so that I may search (blast) the data set for a specific 16s sequence.
I have read through the tutorial, but I am confused about which files to use for this command. In the example provided on the wiki sop page (below), I am wondering which .list file and .fasta file do we use? I have generated one .list file by running through the standard pipeline, is this what I should use? When I viewed the amazon.fasta file in the tutorial, it showed each otu and its sequence; how do I generate that?
get.oturep(phylip=98_sq_phylip_amazon.dist, list=98_sq_phylip_amazon.an.list, fasta=amazon.fasta)