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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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Could you recommend some tools/platform to directly generate the SV breakpoints from Hi-C data, and can be used by NeoLoopFinder? #5

Open wzhang42 opened 3 years ago

wzhang42 commented 3 years ago

Could you recommend some tools/platform to directly generate the SV breakpoints from Hi-C data, and can be used by NeoLoopFinder? I prefer to simple or linux command line format.

XiaoTaoWang commented 3 years ago

I generally use hic breakfinder (https://github.com/dixonlab/hic_breakfinder) to identify SV breakpoints from Hi-C. And after you have obtained those *.breaks.txt files with hic breakfinder, just run the prepare-SV-breakpoints.py script (https://raw.githubusercontent.com/XiaoTaoWang/NeoLoopFinder/master/scripts/prepare-SV-breakpoints.py):

python prepare-SV-breakpoints.py <break_file_from_hic_breakfinder> <output_file_path>
wzhang42 commented 3 years ago

Thanks. Hic_breakfinder require three separated files. Whether it can only need one Hic .cool file? just as the calculate_cnv in NeoLoopFinder did? I only have the .cool file.

JSegueni commented 2 years ago

The other files are the expected inter and intra interactions and you can find them here for the human genome: https://salkinstitute.app.box.com/s/m8oyv2ypf8o3kcdsybzcmrpg032xnrgx

XiaoTaoWang commented 2 years ago

Hey guys, we recently developed a new method EagleC (https://github.com/XiaoTaoWang/EagleC) for predicting a full range of SVs from Hi-C and other 3C-based platforms. The only required input to EagleC is an .cool/mcool file. EagleC does not rely on the background/expected values, so can be applied to any species in theory. Please have a try and let me know if your have any questions. Thanks!