combiz/scFlow

Add a "auto" option for the retain parameter of emptydrops

combiz opened this issue · 0 comments

The in-built retain calculation obtained by setting retain = NULL relies on a barcode rank knee estimate which can be suboptimal for some samples. Another approach, used by cellranger, is to specify how many cells we expect in a sample (e.g. 3000) then to calculate the 99th percentile counts for these cells (m) and to retain any cells with more than m/10 counts.