<p>That's a completely normal way to plot correlation between them. Spearman correlation was a wise choice on your part, since it's rank based and you don't have to care as much about normalization.</p>

<p>Update: It turns out that matplotlib is broken and I need to have a new deepTools release to work around that. That should be available sometime Sunday.</p>

CC BY-SA 4.0
2020-04-04T22:30:30.590Z
here is the file.  Thanks much   https://drive.google.com/open?id=1wKuHg3IfJWBCUwrInk4UZIA7mO80Pl7U
Mariam
CC BY-SA 4.0
2020-04-04T22:39:17.097Z
I suspect this is a matplotlib bug, I'll investigate.
Devon Ryan
CC BY-SA 4.0
2020-04-04T22:55:27.557Z
There's a matplotlib bug that I need to program around. The fix is very simple and I'll release a new deepTools versions as soon as possible (sometime Sunday).
Devon Ryan
CC BY-SA 4.0
2020-04-04T23:14:39.583Z
Thanks alot looking forward to it
Mariam
CC BY-SA 4.0
2020-04-05T06:57:31.080Z
3.4.2 is now on pypi and will be available via conda sometime today.
Devon Ryan
CC BY-SA 4.0
2020-04-06T21:10:08.763Z
Much appreciate.
Mariam
CC BY-SA 4.0
2020-04-04T21:09:02.700Z
2020-04-04T22:54:28.787Z
2020-04-04T22:54:28.787Z
Devon Ryan
<p>I have several mab files from medip-seq. They are supposed to be replicates and I have to draw their correlation. First I used multiBamSummary from deeptools to merge all the bam files based on bi/bed. Now when I am using the plotCorrelation I do not get any file. The argument is:</p>
<pre><code>plotCorrelation --corData myMultiBamSumary.npz --corMethod spearman --whatToPlot scatterplot --skipZeros --removeOutliers --plotFile Myplot --plotFileFormat pdf
</code></pre>
<p>Is that the correct strategy to plot the correlation? Is there any suggestion?</p>

<sam><phylogenetics><sequence-analysis><chip-seq><deeptools>
plot correlation between several bam files
# plot correlation between several bam files

(Asked by: username_0 on 2020-04-04)

I have several mab files from medip-seq. They are supposed to be replicates and I have to draw their correlation. First I used multiBamSummary from deeptools to merge all the bam files based on bi/bed. Now when I am using the plotCorrelation I do not get any file. The argument is:
plotCorrelation --corData myMultiBamSumary.npz --corMethod spearman --whatToPlot scatterplot --skipZeros --removeOutliers --plotFile Myplot --plotFileFormat pdf

Is that the correct strategy to plot the correlation? Is there any suggestion?

**Tags:** sam, phylogenetics, sequence-analysis, chip-seq, deeptools

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## 1 answers

### Answer by username_1 on 2020-04-04. Score: 1

That's a completely normal way to plot correlation between them. Spearman correlation was a wise choice on your part, since it's rank based and you don't have to care as much about normalization.

Update: It turns out that matplotlib is broken and I need to have a new deepTools release to work around that. That should be available sometime Sunday.

> **Comments:**
> **username_0**: here is the file.  Thanks much   https://drive.google.com/open?id=1wKuHg3IfJWBCUwrInk4UZIA7mO80Pl7U  
> **username_1**: I suspect this is a matplotlib bug, I'll investigate.  
> **username_1**: There's a matplotlib bug that I need to program around. The fix is very simple and I'll release a new deepTools versions as soon as possible (sometime Sunday).  
> **username_0**: Thanks alot looking forward to it  
> **username_1**: 3.4.2 is now on pypi and will be available via conda sometime today.  
> **username_0**: Much appreciate.  

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