I have used dada2 denoise-paired to process my data. The quality of my reads was quite high, which is why I decided not to truncate/trim any reads. I’m using the following parameters.
qiime dada2 denoise-paired
Looking at my denoising stats table, I don’t see any reduction from
“filtered” to “denoised”.
These are the average relative number of sequences retained with each step, compared to the input:
Denoised: 79.33% <- no reduction
Why is there no reduction from “filtered” to “denoised”? Is it because of the parameters I used?
In layman’s terms, what is happening during the denoising step?