Hi @Dorothy, sorry about the late reply.
There isn’t a standard protocol for filtering features, but we recommend filtering out features that don’t contain much information.
By that I mean
- Features that have few reads (i.e. less than 10 reads across all samples).
- Features that are rarely observed (i.e. present in less than 5 samples in a study).
- Features that have very low variance (i.e. less than 10e-4)
Of course, these numbers will fluctuate based on the number of samples present in the study.