For eg, you have Sc aligned to both human and mouse genome, how do you then only look at human genes? subsetting only genes with GRCh38 + mito genes (MT-) from a mix? The issue with looking at a combination sc, the mito genes are not getting recognised which is very strange. Not sure how to go about that?
I think that if you want to mix species in one analysis you need to find orthologs first, e.g. find human ortholog for each murine gene. You also have to consider that human and mouse genes have different naming convention, so % mito calculation will not work if you simply merge the objects (i.e. MT vs Mt).