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I have several mab files from medip-seq. they 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 pot the correlation? Is there any suggestion?

Thanks alot

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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.

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  • $\begingroup$ here is the file. Thanks much drive.google.com/open?id=1wKuHg3IfJWBCUwrInk4UZIA7mO80Pl7U $\endgroup$
    – Mariam
    Apr 4, 2020 at 22:30
  • $\begingroup$ I suspect this is a matplotlib bug, I'll investigate. $\endgroup$
    – Devon Ryan
    Apr 4, 2020 at 22:39
  • $\begingroup$ 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). $\endgroup$
    – Devon Ryan
    Apr 4, 2020 at 22:55
  • $\begingroup$ Thanks alot looking forward to it $\endgroup$
    – Mariam
    Apr 4, 2020 at 23:14
  • $\begingroup$ 3.4.2 is now on pypi and will be available via conda sometime today. $\endgroup$
    – Devon Ryan
    Apr 5, 2020 at 6:57

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