Heatmap using Interaction/HiCHip data
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3.6 years ago
pixie@bioinfo ★ 1.5k

Hello, I have two interaction files for two different stages S1 and S2 as obtained from HiCHip data and have analysed it. I have associated Gene annotations to the chromosome regions wherever possible. I want to plot contrasting interaction profiles which are lost/gained in the two stages, but not sure where two start from

My interactions are in this form

Chr1 Start End Chr2 Start End Gene1 Gene2 Some_Score(q value/z-score)

As an example, I have attached an image from the paper Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Rubin et al., Nat Genet. 2017 Oct;49(10):1522-1528. doi: 10.1038/ng.3935. Epub 2017 Aug 14. Any leads will be very helpful.

<strong>Title of the image</strong>: Heat maps of CHi-C q scores (determined by CHiCAGO) for 1,975 enhancer contacts gained with target promoters during epidermal cell differentiation. Contacts are sorted in order of enhancer–promoter (EP) distance

ngs heatmap • 756 views
Entering edit mode

Please see How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)


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