Seleting trunc length to allow Dada2 merge

Thank you for sharing that information.

With that data, we can do the math:

No truncation: 250 + 250 - 465 = 35 bp overlap
With --p-trunc-len-f 245 --p-trunc-len-r 240: 245+240-465=20 bp overlap.

These overlap values are both long enough, but more reads will probably join if you truncate off the low quality bases at the end.

What --p-trim-left-f and --p-trim-left-r do you plan to use?