running HICCUPS on CPUs or GPUs

[tan...@gmail.com]

Dear all, and Dear Neva, 

if i may add a tiny little question please : could we run the pipeline HiCCUPS on CPUs ?

during the initial tests, i am receiving a message : 

"HiCCUPS : GPUs are not installed so HiCCUPs cannot be run"

thank you very much !

[zqzne...@gmail.com]

Hi, 

That means GPU configuration is needed. Instead, you can try the CPU version:

https://github.com/aidenlab/juicer/wiki/CPU-HiCCUPS

Johnson

[Muhammad Saad Shamim]

Alternatively, you could also upload the hic file to Google colab (free) and run hiccups there with the GPU.

Example notebook here:

https://colab.research.google.com/drive/1XelZowBWxBghSyS11rvs90Zmazsj_HPh?usp=sharing

- Muhammad Saad Shamim

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[Bogdan Tanasa]

Thanks a lot for your suggestions !

shall any other jupyter notebooks be  available for HIC analysis, please do not hesitate to let me know ! thanks a lot !

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[Muhammad Saad Shamim]

Here's a link to a colab notebook for using straw to stream hic data to python/numpy.

https://aidenlab.gitbook.io/juicebox/accessing-raw-data

- Muhammad Saad Shamim

[Bogdan Tanasa]

wonderful, thank you very much !