I am using dada2 for filtering: it removes more than 70% from my reads and I want to relax the parameters: Do you have any idea which parameters should I relax?
Currently I am testing these ones:
–p-maxee 3.6 ( but I do not know what is the best error rate to fix and that recover maximum of my reads?).
Also I want to relax maxN per sequence: I want to allow one N in my sequences, but I can’t find this in --help option. Do you know how to include maxN in my parameters?
–p-chimera-method: do you have any suggestion which one is the best: pooled or consensus?
My aim is to relax the parameters so I can recover most of my reads. thanks a lot.