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XiaoTaoWang / NeoLoopFinder

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes
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Custom enzyme list #24

Closed mt96stanley closed 2 years ago

mt96stanley commented 2 years ago

Is there any way to use custom enzymes or fixed bin size for Micro-C / Hi-C 3.0? Thanks.

DittmanC commented 2 years ago

A follow-up question, if I used OmniC, instead of restriction enzyme-based, probably they used DNase I, which is a sequence-independent endonuclease, how can I tune the parameter for calculate-cnv?

XiaoTaoWang commented 2 years ago

Hi all, I just updated the package (0.2.4) by adding an "uniform" option to the "--enzyme" parameter. basically, this option assumes every Hi-C bin contains the same number of fragments. I know it might not be a perfect solution for Micro-C, but if an enzyme is ideally sequence independent, I would suggest you setting "--enzyme uniform" when you run calculate-cnv.

To update your package, just run "pip install -U neoloop".

let me know if you have any questions.

Best, Xiaotao

DittmanC commented 2 years ago

thanks for the updates