Answers.Body: <p>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.</p>
  
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Answers.CreationDate: 2017-06-07T06:15:01.453Z
Answers.LastActivityDate: 2017-06-07T06:15:01.453Z
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Body: <p>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.</p>
  
  <p>What am I missing?</p>
  
Tags: <ngs><bed><metagenome><homer>
Title: What's the scaling for HOMER metagenes?
ThreadText: # What's the scaling for HOMER metagenes?
  
  (Asked by: username_0 on 2017-06-07)
  
  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?
  
  **Tags:** ngs, bed, metagenome, homer
  
  
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  ## 1 answers
  
  ### Answer by username_0 on 2017-06-07. Score: 4
  
  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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