plotProfile with mean of bigwig files

Question

[ildem]

Dear all,

I have 9 bigwig files for which i computeMatrix over a single bed file (deeptools). Say they are replicates of the same experiment (3 replicates of condition1,2 and3). I can then draw a profile plot for all these 9 bw files over this bedfile with plotprofile --pergroup.

Is there a way to draw a plot with the same bed file but taking the mean of all 9 bw files? (i.e. to draw a single line representing all 9 bw files) Or say, taking the mean in groups of 3? ( condition1,2 and3)

without having to make a merged bigwig...

thanks..

[Devon Ryan]

There's no way to do that directly with deepTools, we usually just make big heatmaps.

[ildem]

thanks Devon, I was just wondering if i missed something..

[sim.j.baum]

You could get the data matrix with the underlying values for each bw file (--outFileNameMatrix). Then calculate the mean value for the respective sites and replicates. I dont know if it would be possible to visualize it back in deeptools then but you could visualize it in R for example.