@ChrisKeefe I'm trying to trim off the lower quality, so that they don't cause dada2 to drop the sample. I thought I was doing that correctly by truncating the forward read at 290 and the reverse read at 270, but when I did so I ended up losing a lot of my samples. Also, I'm not sure how to interpret the Dada2 denoising stats. I'll try to do some digging on that that may help me understand what is wrong in my parameters. Thank you for the help!
Best,
Collin