3 Negative Controls - What is the best way to filter my samples and not delete important data from them

[Nicholas_Bokulich]

Hi @Manuela_Ramalho,

@Manuela_Ramalho

I believe that this way I I am deleting an important part of my data

I agree. There is indeed no consensus on the "best" methods. If there is any consensus, though, it is that filtering out anything found in negative controls by default is a bad idea. See this discussion for more details:

Discussion: methods for removing contaminants and cross-talk

Just to add further to this discussion, I've previously used decontam prior to it being incorporated into QIIME 2, and whilst I'm a huge fan of the principles it's built around, it didn't work fantastically for my samples. I will caveat that as I did only attempt the prevalence method with 2 negative controls (one kit negative and one sequencing negative) for around 20 samples, which is likely too low a number of controls to have any real statistical power, I'm not sure what the ideal number of …