I am just starting with Bioinformatics so feel free to tell me if this topic doesn’t belong here.
I am wondering why is normalization function in scnapy (pp.normalize_total) based on total counts in single cell?
My goal is to find SVGs in a given dataset and I am not sure if normalizing by cell is helpful (or even harmful) for my task. It seems logical to me that I should normalize by gene column. It seems to me that each cell should have same sequencing depth so there is no reason to normalize by cell or am I wrong?