I am processing my pacbio 16S rRNA reads through denoise-ccs and as stats-dada2.qzv (1.2 MB)
you can see from the table I am losing almost 60% of my reads at the denoising step. Could anyone help me to improve this? I have tried changing the --p-max-ee but that does not help..
The go to place to start when you are losing more reads than you expected, is to really double check that all non-biological sequences have been removed from your reads, so that is a good place to start. You also might want to watch these videos from one of our workshops about both the theory of denoising and actually running the tools: Lecture & Plugin Tutorial.
However, in your case, I think it likely due to something we are not aware of yet in regards to how DADA2 processes CCS reads, could you try removing --p-min-len and --p-max-len and see if that helps?