filtering data based on total ASV frequency

Hi,

could you please suggest at what step should we do filtering based on ASV. Is it good to do filtering after dada2 step based on frequency?

Kind Regards
Yogesh

Hi @Yogesh_Gupta,
That really depends on what you are trying to do. In some instances removing rare features is advised and even required for the tests to work properly. For example in differential abundance tools like ANCOM and gneiss, rare taxa do not provide any useful information and create noise in the overall dataset so the filtering is recommended. On the other hand, when calculating various alpha and beta diversity measures, these same features can provide valuable information so filtering is not desirable.
You’ll want to customize your workflow to the question you are asking.

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