@ebolyen Thank you for the response.
I think that there are two possible options that I might use (either phylogenetic placement or a little hand wavy taxa collapse). I have a few more questions for both in order to move forward. I have been reading a few forums about the different ways to develop SEPP reference databases. Specifically these ones have been the most helpful so far:
One question I have is in one of the forums it talks about trimming the reference alignment while others say you should not. I would ideally use the Silva138 reference (either 138.1 or 138.2). If I need to trim it that would not be ideal becuase I would want the entire 16S reference file since my different amplicons are from different regions. I am assuming therefore it is okay to not trim the reference file?
I am also wondering how I would create one seq file for all of my different sequences. If I were to run the following commands how would I create one rep-seq.qza file from all my different sequences from different amplified regions:
qiime fragment-insertion sepp
--i-representative-sequences rep-seqs.qza
--i-reference-alignment aligned-rep-seqs.qza
--i-reference-phylogeny rooted_tree.qza
--o-tree insertion-tree.qza
--o-placements insertion-placements.qza
qiime fragment-insertion classify-otus-experimental
--i-representative-sequences rep-seqs.qza
--i-tree insertion-tree.qza
--i-reference-taxonomy ref-taxonomy.qza
--o-classification taxonomy.qza
For taxa collapse I am wondering if there is a way to keep the correlating ASV labels that you would lose after collapsing the taxa file?
Thanks!