Hello @Micro_Biologist,
Not a problem.
I will tackle your main question first, then circle back to the other questions/comments in your post:
It sounds like what you are looking for is feature-table merge
. That allows you to merge multiple feature tables into one, so long as those feature tables are already imported into QIIME as FeatureTable[Frequency]
artifacts. Check out the other merge-*
methods in q2-feature-table
to learn how to merge feature data (sequence or taxonomy) files.
I trust you have found this tutorial on using vsearch to cluster to OTUs (I realize that's not your question, just trying to point out relevant docs in case you haven't spotted them)
Perhaps I misunderstand — but you would still be able to compare sequence variants, e.g,. the output of dada2 and deblur, with OTUs. Sequence variants are in a sense OTUs clustered at 100% similarity. (you can also use q2-vsearch
to cluster into OTUs following dereplicating/denoising with deblur/dada2, thereby getting the denoising benefits of these methods while still clustering into OTUs).
Just to get a working pipeline any data would do — so the moving pictures data is fine. But for comparing your pipeline to older methods, you may want to consider using mock communities or other test datasets with known composition to assess how well your pipeline performs relative to another "gold standard" method.
Of course! That's what we're here for.