Generating a strand specific heatmap of ChIP-Seq Data

Question

[Sam]

I am under the impression that if my strand information for my region file is on the 6th column then computeMatrix takes orientation into account.

Is there a way I can generate a strand specific heat map where for example the Watson strand is Red and the Crick strand is blue? Preferably using something like deeptools.

The TF I am hoping to do this with is Pol-II at TSS.

[Asaf]

Can you IP polII with a specific strand?

Answer 1

[Fidel]

You can make two groups of TSS, one containing only one strand. Then you can plot the profile for each strand on different colors using profiler. Alternatively, you can run computeMatrix twice, once with the Watson and the again using the Crick strand. Then can make heatmaps for each case using the colors that you want.