There’s many question about this type of data from ion torrent metagenomic kit.
Question 1: Raw sequences contain primers and they are about the 20 first and last bases of each sequence (with variants). Primers are not informed but it is possible to deduct them from raw sequences dataset. You can then separate each region with cutadapt.
The bigest question remaining for me is how to integrate the dada2 preprocessed dataset from each variable region? (like question question 4. @MiriamGorostidi) sum abondance of the same taxa taken from different regions seems not norrect to me. or the only way is to analyze each region separately?
I have read this interesting dicussion of @cjone228 but no real answer to this part.