Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-04T22:30:30.590Z
Answers.Text: here is the file.  Thanks much   https://drive.google.com/open?id=1wKuHg3IfJWBCUwrInk4UZIA7mO80Pl7U
Answers.UserDisplayName: Mariam
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-04T22:39:17.097Z
Answers.Text: I suspect this is a matplotlib bug, I'll investigate.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-04T22:55:27.557Z
Answers.Text: 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).
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-04T23:14:39.583Z
Answers.Text: Thanks alot looking forward to it
Answers.UserDisplayName: Mariam
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-05T06:57:31.080Z
Answers.Text: 3.4.2 is now on pypi and will be available via conda sometime today.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-06T21:10:08.763Z
Answers.Text: Much appreciate.
Answers.UserDisplayName: Mariam
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-04T21:09:02.700Z
Answers.LastActivityDate: 2020-04-04T22:54:28.787Z
Answers.LastEditDate: 2020-04-04T22:54:28.787Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Tags: <sam><phylogenetics><sequence-analysis><chip-seq><deeptools>
Title: plot correlation between several bam files
ThreadText: # 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
  
  
  ---
  
  ## 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.  
  
  ---
  
  