I am trying to determine the sex of a mouse for an RNA-seq experiment. If I do CPM normalization using edgeR and observe many chromosome Y genes displaying CPM > 0, then is it safe to assume the mouse is a male?
Probably, but the surest way to recognize the sex of the mouse is to examine the expression of Xist on the X chromosome. Xist is very highly expressed in all female cells (regardless of cell type or cell state) and not at all male cells, so it is a sure thing. We use it as a routine check in all our mouse RNA-seq analyses. Xist RPKM is usually >20 (often>100) in females and <1 in males.