DADA2 truncated low quality region

Yes, I agree with your conclusion!

Let us return to the first question:

I usually run DADA2 several times with different --p-trunc-len—* settings and select the ones that allow most of my data to merge successfully.

Now that you have run DADA2 twice, try running it a few more times to maximize the values in the "percentage of input merged" column! Your coworker found good settings already, so see if you can find even better ones!

For a detailed discussion of how to choose DADA2 truncation settings, see: