Hi @lindd,
No problem!
This is a question I've been pondering for a while now myself. The short answer is, no there are no real criteria to follow as far as picking your truncating parameters go, perhaps some guidelines though. See this explanation that may help you decide.
In general, you want to keep the length of reads as long as you can without allowing too many poor reads. I've heard on this forum that keeping the median above a score of 20 is a good starting point. Luckily your reads look pretty good to me so your current parameters are probably ok and long enough for an overlap to occur.
I'm not entirely sure I understand what you mean by this, could you clarify this please? If you are referring to your barcodes and adapter sequences, you have to make sure sure you have removed those prior to DADA2. This is very important, otherwise those 'non-biological' sequences will force most of your reads to be discarded. If the barcodes are all the same length you can use the --p-trim option to remove them easily.