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anyuzx / HIPPS-DIMES

Maximum Entropy Based HI-C/Distance Map - Polymer Physics - Structures Method
MIT License
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Is the entire genome reconstruction feasible? #4

Closed Huang-XN closed 7 months ago

Huang-XN commented 7 months ago

Hi @anyuzx,

Thank you for this wonderful tool.

In the example, the tutorial showed reconstructing the 3D conformation for only one chromosome using HiC contact map. I was wondering if HIPPS-DIMES could do it for the whole genome instead of one chromosome based on HiC data.

Thank you. Hope you could answer it.

Best, Xingnan

anyuzx commented 7 months ago

Hi Xingnan, unfortunately, the model has not been tested for reconstructing the multiple chromosomes. If you provide the contact map that contains multiple chromosomes, in principle, the model will generate structures. However, we have not tested whether the reconstructed structures are reasonable or not.

Huang-XN commented 7 months ago

Thank you for your reply. I will try it.