I have been given three files from Illumina sequencing (forward, reverse, and barcodes with the emp protocol) after being hired onto a project with no QIIME analysis experience.
My method has been to use q2studio platform to demultiplex and quality filter the sequences, then use dada2 to pick otus/sequence variants, and am now trying to navigate how to do downstream analysis and was hoping someone would have an idea of what path to take.
The files I have been given are from many samples taken at 7 different sites, and two types of samples within each site. I am wanting to find the relative abundance of a specific genera of bacteria between the sample types within each site, and compare them across all sites.
Between assigning taxonomy, filtering the tables, and deciding whether to filter sequences, samples, or features, I am confused and a little overwhelmed with what to do. I am happy to provide more information if that would help!
Thanks so much.