Question: Generating a strand specific heatmap of ChIP-Seq Data
0
gravatar for Sam
3.9 years ago by
Sam70
United States
Sam70 wrote:

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.

heatmap chip-seq deeptools • 1.6k views
ADD COMMENTlink modified 3.9 years ago by Fidel1.9k • written 3.9 years ago by Sam70
1

Can you IP polII with a specific strand?

ADD REPLYlink written 3.9 years ago by Asaf6.4k
1
gravatar for Fidel
3.9 years ago by
Fidel1.9k
Germany
Fidel1.9k wrote:

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.

ADD COMMENTlink written 3.9 years ago by Fidel1.9k
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