plot correlation between several bam files 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
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.