mothur

How do I get unique seqs from mothur output files in R (phyloseq)

Hi, i’m new to microbiome analyses. I’ve got 4 output files from mothur:

  • stability.an.0.03.subsample.groups
  • stability.an.0.03.subsample
  • stability.an.cons.tax
  • stability.an.cons
    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?
    Thank you!

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