Thanks @antgonza. I tested different truncation and maxEE so that part is fine with me. My question is rather about the length of sequences that get merged/passed quality trimming. For example, we see in the summary table (after run dada2 denoise-paired command) we have X number of "total frequences" which reflect how many pairs were merged/passed quality trimming. Can we know what are the lengths of this X number of sequences? I guess an easy way is to say: what are the lengths of these fastq/fasta? I read on another thread that we can't export fastq file after the dada2 denoise step (again, I know we can get representatives easily). If there is a report or summary of the total pool of sequences it could be useful, too.
From your reply it looks like the representative sequence is all I can get (in terms of the length and actual sequences). Let me know if I interpret it wrong.
Thanks very much for your help and explanation!