Restriction enzyme free HiC

GaoLabXDU / HiSV

HiSV: a computational pipeline for structural variation detection from Hi-C data

MIT License

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Restriction enzyme free HiC #6

Open torchij opened 11 months ago

torchij commented 11 months ago

Hi, in the SV_type module, a RE_file is required, however, what should one do if we do not use restriction enzymes? For example Mnase or Dnase digestion?

Many thanks!

GaoLabXDU commented 11 months ago

Hi, this is a very good question!

We have modified the code of the SV_type module. If RE is not used in Hi-C experiments, the user can enter --withoutRE so that the program does not consider the RE site when normalizing the coverage profile.

You can install the latest version of HiSV via this code (pip install hisv==1.0.9)

I hope my answer can help you. If you have any questions, please let me know.

torchij commented 10 months ago

This is amazing, thanks for getting back so fast!