Heatmap ChIP-seq average signal

Question

[Marco Pannone]

Hey everybody!

I am aiming to generate a heatmap for the average signal of a certain histone mark across all gene coding regions, with TSS as the reference point.

I am already aware of how to produce such plots using plotProfile and plotHeatmap from the deeptools package, and I can obtain the desired results with an average profile plot.

However, I wonder if I can visualize the same by using a heatmap instead.

I would like the heatmap for each sample to be just one row, rather than multiple rows depending on how many regions are in the coordinates file, with the average signal across all those regions provided.

Not sure if it was clear enough and if there is a way of doing so with deeptools or other tools.

Thanks in advance for the help!

Answer 1

[bk11]

Please try Complexheatmap & EnrichedHeatmap. You can see in the link below how it can be done-

http://jokergoo.github.io/EnrichedHeatmap/index.html

[Marco Pannone]

Thanks for the answer but it does not solve my question. I know both those tools and they do nothing more than the ones I mentioned from deeptools, at least about plotting ChIP-seq signal.

[Trivas]

If I remember correctly, deeptools spits out the matrix used to generate the histograms. You could normalize each region within each sample (e.g., 0-1) then average across the regions within each sample, then plot as a heatmap.

However, depending on how many samples you have, a histogram of the average signal could be easier to interpret, especially if you're trying to visualize peaks shifting up or downstream or even magnitude. Take a look at some of the options in the Homer suite of tools (annotatePeaks.pl) as they do a lot of this for you.