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yezhengSTAT / FreeHiC

FreeHi-C pipeline for high fidelity Hi-C data simulation.
MIT License
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How to use FreeHiC to simulate structural variation? #9

Open TomWang666 opened 8 months ago

TomWang666 commented 8 months ago

Hello, I am currently using FreeHiC in my work and I would like to simulate some structural variations on GM12878. How should I set parameters to simulate multiple different types of structural variations? Looking forward to your reply！

yezhengSTAT commented 8 months ago

FreeHiC algorithm itself cannot create structural variations, but you can provide structural variation Hi-C matrix as a reference, and FreeHiC can simulate according to the reference map adding randomization. If you need multiple different types of structural variation, you will need to provide multiple reference contact matrices with different types of structural variation.

Hope it helps.

Thanks, Ye