Hello Julie,
The dada2 developers recommend running dada2 on each run separately then combining the results, which is a perfect fit for your data set. Even better, the dada2 denoise-paired command comes with two --p-trim-left
commands for trimming off the start of your 341 read so it starts around 515!
Take a look at that command and let me know if it looks like a good fit for your data.
Analyzing a consistent region is important and I’m glad your post will raise awareness of this for future users.
Colin