DADA2, truncation lengths and features number

[mchialva (Matteo Chialva)]

@benjjneb

That does require doing some simple balancing yourself between those priorities (must maintain overlap, but get rid of post-crash bases) but usually it’s pretty easy to pick something reasonably good. And if not, we are happy to help (but please post the quality profile of your reads and your amplicon setup in that case).

Thanks a lot for your really clear explanation. As you suggested I look at quality profiles and I observed a consistent drop-off in quality at reverse reads. My amplicons are 341f-805r so should be about 460 bp.

Looking at profiles I would truncate reverse reads at 220-240 but I'm not sure what is the minimum acceptable overlap between reads. 50-60 bp might make sense? A different left reads and right reads truncation value would be acceptable?
Thanks again!