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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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input with mouse cells #19

Closed skytguuu closed 2 years ago

skytguuu commented 2 years ago

Hi,

I was wondering whether this tool worked in mouse or not? It seemed need hic_breakfinder's output file, however, hic_breakfinder only support the expect file in human.

Could you give me a hand?

Thanks

XiaoTaoWang commented 2 years ago

Yes, hic_breakfinder can only detect SVs in human cells; but NeoLoopFinder should work for mouse cells as well once you have an SV list.

skytguuu commented 2 years ago

Thanks for your help. Indeed, NeoLoopFinder could work for mouse cells, however it need "K562-test-SVs.txt" file, which I thought came out frome hic_breakfinder output. Am I undersanding right? How can I get the input file of assemble-complexSVs?

Thanks

XiaoTaoWang commented 2 years ago

Yes, you are right. I'm sorry but as far as I know, there's no software that can detect SVs from Hi-C map of non-human cells.

skytguuu commented 2 years ago

I see, thanks for your explanation.

Thanks!