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combiz / scFlow

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.

Home Page:https://combiz.github.io/scFlow/

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

combiz opened this issue · comments

commented

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.