bamCoverage --normalizeUsing RPKM
does the normalization using a constant bin size. Afaik, the standard normalization using RPKM uses the length of the specific gene (not constant).
So does --normalizeUsing RPKM
really represent the standard RPKM normalization (done with the gene length)? What is it purpose, if not?
In "classic" RPKM the gene length varies from gene to gene, doesn't it? Whereas in Bigwig normalization the bin size is constant (and many short bins can be included with one gene).
So the bottom line is that the RPKM (and CPM) does not really represent the "classic" RPKM/CPM, right?
CPM does represent the standard approach I think, as it simply divides by total depth and multiplies by a million.