<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>

CC BY-SA 4.0
2020-12-28T16:27:27.863Z
2020-12-28T16:27:27.863Z
Devon Ryan
<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>

CC BY-SA 4.0
2020-12-29T08:36:44.450Z
If I'm not mistaken, RPKM includes a "normalization" by unit of length, so it does not make sense to sum these values along a region. A weighted average makes more sense (were the weights would be the bin widths).
bli
<rna-seq><deeptools>
Clarification regarding (deepTools) bamCoverage output
# Clarification regarding (deepTools) bamCoverage output

(Asked by: username_0 on 2020-12-28)

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?

**Tags:** rna-seq, deeptools
> **Comments:**
> **username_1**: If I'm not mistaken, RPKM includes a "normalization" by unit of length, so it does not make sense to sum these values along a region. A weighted average makes more sense (were the weights would be the bin widths).  

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## 1 answers

### Answer by username_2 on 2020-12-28. Score: 3

1. Yes
2. 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.


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