The goal of this tutorial is to demonstrate basic analyses of microbiota data to determine if and how communities differ by variables of interest. In general, this pipeline can be used for any microbiota data set that has been clustered into operational taxonomic units (OTUs).
The goal of this tutorial is to demonstrate standard operating procedures (SOP) for processing amplicon data that are generated using Illumina's MiSeq platform with paired end reads. This SOP is a combination of the Schloss lab and Suen lab (UW-Madison) procedures for 2x250bp reads of the V4 region of the 16S rRNA gene. The original Schloss SOP can be found at http://www.mothur.org/wiki/MiSeq_SOP. Published work using this SOP should cite https://www.ncbi.nlm.nih.gov/pubmed/23793624
Materials for the Spring 2017 "Microbiota Analysis in R" workshop at the U. of Wisconsin-Madison Bioinformatics Resource Center (BRC).