where to truncate reads in DADA2?

Hello everyone,

Hey guys, I've just started to get the hang of qiime2 but I am having trouble deciding were to truncate the reads in DADA2, especially. I have attached the screenshot as shown

The quality of the forward reads look good whereas the quality of the reverse end reads is lower and I don’t know where to truncate. I'd really appreciate if anyone could provide me with support. For the forward reads I was thinking of triming 62 from the left and a trunc of 280 and for the reverse reads trim left 62 and trunc 250. My worry is the parameters I selected could lead to overtrim/undertrim.

Welcome to the forum, @goipil!
Your trimming parameters will depend on how long your target amplicon is. In order to join forward and reverse reads, current versions of DADA2 require at least 12 base pairs of overlap in addition to full coverage of your amplicon. (F + R >= amplicon-length+12)

There are other factors to consider (padding to accomodate natural variation in sequence length, not trimming left to support easier meta-analysis, etc.), and this subject has been covered at great length on this forum. Take some time with the search :mag: feature, and I suspect your questions will all be answered. If you have any more-detailed questions on this subject, feel free to reply to this topic.

All the best,
Chris :elephant: