XiaoTaoWang/NeoLoopFinder

Custom enzyme list

mt96stanley opened this issue · 3 comments

mt96stanley commented

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

DittmanC commented

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

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

  • 👍1
DittmanC commented

thanks for the updates