I got stuck in a dead-end path. I need your guidance.
I have been analyzing a functional gene for a couple of months. The result was unacceptable with the database extracted from NCBI because there were too low defined taxa. Today, I blasted the rep-seq with BLASTx. The result made my day. Now, I need to switch to protein analysis instead of DNA-based analysis, and also I need to know how can I work with protein sequences by QIIME2. I believe that no one has started such a thing with Qiime2. Anyway, It needs a protein database instead of DNA one. And I have only DNA sequences and OTUs table in available, generated with DADA2.
Can I analyze a functional gene in QIIME2 with a protein database?
Can I extract protein database with the Rescript plugin in Qiime2?
And eventually if I start my analysis based on a protein database, how can I deal with the feature-table and ref-seq obtained DADA2, which they are constructed based on DNA sequences?
Please share your valuable suggestion with me.
Thank you very much.