Woodrat experimental diet analysis

This includes example code used for processing 16S rRNA sequences derived from woodrat foregut and caecum contents

The QIIME2 portion of the workflow includes commands used in shell environment

QIIME2 artifacts are then imported into R for statistical analysis

To generate a manifest file for qiime, run the make_manifest bash script in the directory where the fastq files are, or provide the directory as an argument when calling the script

bash make_manifest.sh . #here I am providing the directory with '.' as this is the directory with the fastq files