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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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Can neoloopfinder applied to mitosis cells? #67

Open Xieeeee opened 3 months ago

Xieeeee commented 3 months ago

Hi Xiaotao, I have a quick question, can the CNV inference be applied to condition with global copy number shifting like mitosis cells? since it is a regression based on read coverage and other factors, and we have to input the default copy number, I guess the answer is no?

Best, Yang

XiaoTaoWang commented 3 months ago

Hi Yang, I agree that using "segment-cnv" could be challenging due to the need for an estimated ploidy value as input. However, "calculate-cnv" should still work for mitosis cells.

Xiaotao