text: user10155: Im using bamCoverage on a file and ive set the bin size to 1 but also normalizing using RPKM for defined regions using a bedgraph file.  The output from bamCoverage however is in binned segments each with a (RPKM) score.  Am I correct in interpreting then that
  1 - the output bedgraph tells me the (total) RPKM score for that particular bin?
  2 - to get the total RPKM score for the region defined in the bedgraph I need to sum all the RPKM scores given for that particular region?
  
  user77: 
  Yes
  The total RPKM for the region in the bedgraph file is the value already present in the bedgraph file. If you want to estimate the RPKM for a larger region composed of multiple bins then you can average the per-bin RPKM values. Note that adjacent bins with the same value are merged by deepTools, so you will need to account for this.
  
  Note that RPKM is NOT a robust normalization and that I should remove it from deepTools so people stop using it.
  
original_text: 10155: <p>Im using bamCoverage on a file and ive set the bin size to 1 but also normalizing using RPKM for defined regions using a bedgraph file.  The output from bamCoverage however is in binned segments each with a (RPKM) score.  Am I correct in interpreting then that</p>
  <p>1 - the output bedgraph tells me the (total) RPKM score for that particular bin?</p>
  <p>2 - to get the total RPKM score for the region defined in the bedgraph I need to sum all the RPKM scores given for that particular region?</p>
   77: <ol>
  <li>Yes</li>
  <li>The total RPKM for the region in the bedgraph file is the value already present in the bedgraph file. If you want to estimate the RPKM for a larger region composed of multiple bins then you can average the per-bin RPKM values. Note that adjacent bins with the same value are merged by deepTools, so you will need to account for this.</li>
  </ol>
  <p>Note that RPKM is NOT a robust normalization and that I should remove it from deepTools so people stop using it.</p>
  