Hi-C contact probability
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Entering edit mode
4.0 years ago
int11ap1 ▴ 430

I was wondering, if I have a Hi-C matrices and the average ICE-normalized interaction vs. genomic distance, how can I create a plot like the following one?

enter image description here

I created something similar:

enter image description here

but it's not contact probability. I want to draw as well the fractal lineal regression.

Thanks

hi-c • 1.8k views
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Hi,

can you solve this problems? I have trouble in this figure. I read the paper about Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome, But I am more confused. So, if you could solve this, could you add a comment? Or how to calculate the frequency is helpful.

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Entering edit mode
6 days ago
LolrenceH • 0

Hi,

I'd like to refer you to Organization of the Mitotic Chromosome, Naumova et al 2013 Science. There is a paragraph about calculating contact probability in supplemental, as well as some references.

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6 days ago

I cant see the first image, but from the second, it looks like you would be better off by doing logarithmic binning. I made that plot (and the log-binned one) using code from this tutorial:

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