Hi @steff1088,
Your workflow looks correct to me; there is also a community tutorial on OTU picking here that may be useful in case you have not already seen it.
I think not, since this is open reference and many of the OTUs will have no associated SILVA ID/taxon. If you used closed reference, that should be possible.
You are using the currently recommended workaround but just FYI soon that feature table could be passed to filter-seqs
directly. See this issue to track progress.
correct
Yes, as long as these OTUs correspond to the 16Sonly_consensus_taxonomy_7_levels.qza
.
Correct! and all other downstream analyses.
I hope that helps! Let us know if you run into any trouble (probably in a separate thread).
Happy QIIMEing