I'm trying to use HOMER to make a metagene profile over gene bodies using a bedgraph file I've generated. The problem is that every time I do, I get really weird scaling on the y-axis. I should be getting average values across the gene body on the order of 5-10, but instead I'm getting values on the order of 0.03-0.05 or less. The weird thing is, when I don't use metagene script or when I don't use histogram with -size given, I get perfectly normal values -- but that's not what I want, unfortunately, for the metagene profile.
What am I missing?