I have extensively read about percent mito in Seurat but I got more and more confused

Let's say we want to keep cells with maximum 20% of their expressed genes are mitochondrial genes, so shall I set percent.mito < 20 or percent.mito < 0.2 or percent.mito < 80 ?


1 Answer 1


Checkout the first Seurat tutorial. To filter cells with >20% mitochondrial counts:

obj[["percent.mito"]] <- PercentageFeatureSet(obj, pattern = "^MT-")
obj <- subset(obj, subset = percent.mito < 20)
  • 1
    $\begingroup$ I tried reading the tutorial and things are not really clear there. @Exhausted, when the tutorial says "we filter cells", they mean filtering them out i.e. removing them. So in the subset call, one needs to state the criteria that the data needs to pass. It's quite clear that the percent is 1-100, not 0-1 though. $\endgroup$
    – Ram RS
    Jul 16, 2021 at 16:42

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