I have some questions about DADA2 truncate low quality region. I would appreciate it if you can help me!
After running ITSxpress, I trimmed the sequences based on the quality plot, but the final output showed very few filtered sequences. However, when my lab mate used the same data and applied the parameters I had used for a previous dataset (because she assumed they didn’t need to be changed), the filtered sequence count was much higher. I wonder how to set the trimming parameters for DADA2? Why did I get so few filtered sequences even though I trimmed based on the quality plot?
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: