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GangCaoLab / CoolBox

Jupyter notebook based genomic data visualization toolkit.
https://gangcaolab.github.io/CoolBox/index.html
GNU General Public License v3.0
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How is insulation score calculation performed? #55

Closed gdolsten closed 2 years ago

gdolsten commented 3 years ago

Would it be possible to export the insulation score to a bigwig?

zhqu1148980644 commented 3 years ago

you can check the source code here: https://github.com/GangCaoLab/CoolBox/blob/6432254cc343ed35e4578eb2d5662cfc59ac09db/coolbox/core/track/hist/hicfeature.py#L184 it's calculated the same way as the original paper.

you can use the "normalize" parameter to get the background normalized insulation score.

For bigwig output, you can use the pybigwig package to manually create the file.

at-katsu commented 3 years ago

Not sure if I missed it, but which original paper are you referring to? Thanks.

Nanguage commented 3 years ago

This is the original paper of the IS method:

Emily Crane 2015. Condensin-driven remodelling of X chromosome topology during dosage compensation