Will filter cell by highly variable genes (HVG) selection marks DGE for the filtered out low variable genes in further analysis?

Question

[point0907]

I want to compare DGE between treated group and control group of single-cell Seq experiment. The genes of my interest are considered to be house keeping genes. In scSeq workflow part feature selection, it is recommended to filter in only the highly variable genes (HVG) (such as FindvariableFeature in Seurat) for further downstream analysis.

My question is: will the HVG feature selection filter out the house keeping genes (which regarded as stable expression genes) therefore negatively impact my downstream analysis of DEG in those genes?

PS: I am a newbie in this field

Thanks in advance!

Answer 1

[ATpoint]

Do you have a reference? HVGs are usually used for clustering and visualization. For everything else use all genes, or those filtered for some minimal expression in x% of all cells or clusters. See the OSCA Bioconductor single-cell book for an awesome read.