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Hi-C contact probability

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
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updated by Juan Felipe Ortiz • Juan Felipe Ortiz • written by int11ap1 int11ap1

2 answers

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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written by LolrenceH • LolrenceH

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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written by Juan Felipe Ortiz • Juan Felipe Ortiz

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