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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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The discrepancies of neoloop results and neotad results #17

Closed wzhang42 closed 2 years ago

wzhang42 commented 2 years ago

Hi, Xiaotao, I have compared the results of neoloops and neotads. I found that neotad report some new thing which is not in the early step neoloops. I am puzzed. My boss also want me to make an explanation. I read through your Nature method papers and other related papers and generally conclude as the two points ( I want your confirmation). 1.) neoloops is based a machine learning module, peakachu. 2.) neotad is not based on machine-learning method , even not based the neo-loop results, but based on a method for DI based boundary detection (your 2017 NAR paper).
Thank you in advance

XiaoTaoWang commented 2 years ago

Yes, you're correct, Neo-loops and Neo-tads are detected using different methods, so it's not a surprise to see they are not the same.

wzhang42 commented 2 years ago

Thank you so much for your confirmation.