Relaxing dada2 parameters

Hi erveryone,

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.


Hey there @Hajar, have you had a good read-through of the DADA2 docs? That will be the best place to get started on honing in these parameters. Keep us posted!

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