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XiaoTaoWang / EagleC

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
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EagleC HiChIP with Neoloopfinder #21

Closed nyuhic closed 1 year ago

nyuhic commented 1 year ago

Hello,

More a question than an issue. I have used EagleC to predict SVs in my HiChIP data and converted it to NeoLoopFinder format. I was wondering if I can use this as input to NeoLoopFinder or not? I know EagleC supports HiChIP data but not sure if NeoLoopFinder does?

Thanks

XiaoTaoWang commented 1 year ago

Hi, sorry for the late response. You may run "assemble-complexSVs" and "neoloop-caller" on your HiChIP data as if it is a Hi-C data by specifying "--balance-type ICE" in your commands. However, applying ICE to HiChIP may eliminate meaningful interactions and induce fake interactions. But I do have a plan this year to release a new version that considers HiChIP's own features. I will keep you posted when it is done.

Best, Xiaotao

nyuhic commented 1 year ago

Thanks, I will try that.

But just to make sure I understand correctly, when using ICE normalized mcools I would skip the calculate-cnv, segment-cnvs and correct-cnvs steps and directly use the assemble-cnv command on my data, right?

XiaoTaoWang commented 1 year ago

Yes, if you are going to use ICE-normalized values to identify neo-loops, you can skip them.

nyuhic commented 1 year ago

Thanks