ScaleData, cell cycle and the choice of features

[SirKuikka]

Hi,

I was wondering if it's ok to specify only the variable genes in ScaleData when regressing out cell cycle.
obj <- NormalizeData(obj)
obj <- FindVariableFeatures(obj,selection.method = "vst",nfeatures = 2000)
s.genes <- cc.genes$s.genes
g2m.genes <- cc.genes$g2m.genes
obj <- ScaleData(obj, vars.to.regress = c("S.Score", "G2M.Score"), features = VariableFeatures(obj))

This is much slower, and this is how it's done in the tutorial
obj <- NormalizeData(obj)
obj <- FindVariableFeatures(obj,selection.method = "vst",nfeatures = 2000)
s.genes <- cc.genes$s.genes
g2m.genes <- cc.genes$g2m.genes
obj <- ScaleData(obj, vars.to.regress = c("S.Score", "G2M.Score"), features = rownames(obj))