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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?

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Figured it out! For anyone who finds this thread in the future and is wondering what is going on: HOMER, when using the -size given option, normalizes the y-axis to the number of basepairs in the intervals -- in this case, the length of the gene body. To get the "raw" values, as I wanted, you need to multiply by the length of the gene body to "undo" the normalization.

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