Hi, i’m new to microbiome analyses. I’ve got 4 output files from mothur:
I’d like to know how can I get the unique number of OTUs in R from these files as well as their phyla and classes. Do I have to convert these files in anyway? Anyone know the codes to run these files in R?
I think you have “hide file extensions” turned on in your file browser because those aren’t the correct extensions. (this is an annoying default in both window and mac).
I don’t use phyloseq, but you can look at the first 100ish lines of my generic R script to see how to read mothur files in without having to alter them. https://github.com/krmaas/bioinformatics/blob/master/Generic.data.exploration.Rmd