I am analysing some ChIP-seq data of a histone modification and different treatments.
I am new on bioinformatics. What I have so far are the peak calling and the differential binding events (using MACS2).
I would like to express the data using a heat map. I have found some papers that use this kind of graph. What I don't understand is what measure is used to generate this graphs, when I do the annotation of the peaks the files comes with genes, start and end sites, peak score (???), distance of the nearest trscription start site, Can I use any of this in my heat maps? What about normalization between treatments? How can I do this?
Thank you
Hi Dalila,
The easiest way of making heatmaps with ChIP-seq data is to use inbuilt tools in Cistrome:
http://cistrome.org/ap/
Just sign yourself up, upload your data and use the different tools on the left hand side.
It can generate both averages (SitePro tool) and heat maps (heatmap tool) under Cistrome toolbox - Integrative analysis - association study.
You need bed files to define regions of interest (peaks) and wig/bigwig files based on which the heatmap will be drawn. It does not do any normalization so this has to be done during creation of the wiggle files.
For the creation of normalized files you can use deepTools:
https://github.com/fidelram/deepTools
Best, Tonis
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