Picking values for --p-min-length and --p-max-length in qiime feature-classifier extract-reads

[Mehrbod_Estaki]

Hi @KQUB,

@KQUB

something like --p-min-length 400 and --p-max-length 450 or --p-min-length 400 and --p-max-length 500 isn't very significant?

I agree with @Deni_Ribicic here, I think in your scenario you shouldn't use such strict parameters. Either don't trim at all (what I would do) or use something relaxed such as @Deni_Ribicic's recommended 400/500. This is especially important when targeting a variable region like the V3-V4, the last thing you want is to introduce bias of a certain clade that is either longer or shorter than your arbitrary parameters.

@KQUB

Do you mean that your current recommendation, when using primers targeting the V3–V4 region, is to set both --p-min-length and --p-max-length to zero?

That's what I would, to be play it safe .