Hi Chloe,
Thank you so much for your help. This is the only sequence data I was provided by the company, for some reason they will not provide the raw reads with the primers and adapters attached. The reads are filtered for barcodes and primers and merged. Unfortunately, when I go through the entire pipeline after using qiime dada2 denoise-single half of the reads in each sample end up being unclassified as these reads are the reverse compliments.
I think because I cannot use the qiime dada2 denoise-ccs with the --p-front option I cannot orient the reads correctly before classification.
Are there any ways around this? I was starting to look into RESCRIPt's orient-seqs command. Additionally, does the Silva data base not include both forward and reverse compliment reference sequences? Does --p-read-orientation both not include both of these sequences for the command qiime feature-classifier extract-reads?
Thank you,
Jackie