I have microbiome data that analyzed by Mothur,
I want to create a file with OTU a representative sequence for analyzing the data in R with phyloseq package following the tutorial of " Analyzing the Mothur MiSeq SOP dataset with Phyloseq"
this command was found “get.oturep(column=final.dist, list=final.list, fasta=final.fasta, count=final.count_table, label=0.03)” to do that, however, “cluster.split” was used instead of the main command in SOP workflow “cluster” thus the output of dist.seqs and cluster are unavailable for me.
My question is how can I get/create this file with the output of cluster.split?
thank you in advanced