I have used the QIIME 2.2019.10 version for my meta-analysis.
Initially, I have download the sequences from NCBI and other databases and separately analyzed them up to DADA2. Then I had merged the files (rep_seq and table) and used q2-fragment insertion plugin (because of different 16S rDNA primers used in the various study) to make a single tree file for phylogenetic analysis.
After that, I used the q2 fragment insertion out files and phylogenetic tree for taxonomic classification, alpha and beta diversity and predicting important feature by Random forest method.
My question is whether this workflow is correct.
Thank you for your valuable time and reply