dada2: trunc len determine

@YuZhang , DADA2 only requires 12 bp of overlap (20 was a requirement a long time ago). Your target amplicon is 806-338=468 bp long. You'll need 12 bp of overlap, so 468+12 = 480. And most 16s amplicons naturally vary by a few bp in length, so it would probably be safest if the length of your truncated f and r reads summed to 483.

The parameters you select will vary depending on your study. Ideally, I aim to truncate when the median q score drops below 30. For high-quality, high-biomass, samples, this is often possible, but your data may not allow that.

If you include positions with low quality scores, you will lose reads during the filtering step. If you truncate too much, you will lose reads during the merging step, because your reads won't join. If you're unclear on this, spend some time reading about choosing DADA2 parameters here on this forum, and look at the original paper preprint, linked in our previous discussion of DADA2.