I'm doing a meta-analysis and one of the studies I included performed 16S 5R sequencing, so I used the plugin q2-sidle to analysis its data, which is amazing and so far I got the results just as I wanted to be.
However, I came across a problem that, when I tried to merge the output rep-seq and table with others using qiime feature-table merge, I got confused of which output of sidle is the rep-seq I should use. Is league-rep-seq-fragments.qza output by command qiime sidle reconstruct-fragment-rep-seqs the rep-seq?
It depends on what you're hoping to do with the representative sequences.
If you want to do fragment insertion, then yes, that would be the appropriate set of sequences.
I'm not sure its the best choice for other applications. The output of reconstruct-fragment-rep-seqs provides consensus sequences only if a reference sequence can't be resolved (ids that have a | symbol in them.) It's designed specifically to integrate with the fragment insertion and makes some downstream assumptions, including that you have the same database and insertion tree version.
The rep-seqs wouldn't be appropriate for use with a naive bayseian classifier, though. (You should do taxonomic reconstruction through sidle.)
If you're thinking about blasting sequences, I think I'd use the original sequence representative sequences from the database as my representative sequence, and then blast both sequences in an unresolved sequence.
I checked feature-table plugin and saw a method merge-taxa, I plan to merge the league_taxonomy.qza output by command qiime sidle reconstruct-taxonomy with other taxonomy.qza I got with naive bayseian classifier.
I'm quite confused by your workflow. The sidle reconstruct-taxonomy is intended to replace naive bayseian classification. (We compared this is on our preprint). Are you doing meta analysis?
