mothur

Representative sequences OTU

Hi everyone
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

Hi,

Sorry, we don’t have anything to do with phyloseq and the mothur team doesn’t use it. I’d strongly encourage you to use to use dplyr and ggplot2 instead since it will allow you to make much nicer figures more easily and will set you up for long term success in generating any type of scientific figure.

You can find a free tutorial for using R with mothur output using functions from these packages here:

https://riffomonas.org/minimalR/

Pat

Thank you for the advice
I will follow it