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ma-compbio / Higashi

single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
MIT License
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some question about json file #28

Closed yangfeizZZ closed 1 year ago

yangfeizZZ commented 1 year ago

Hello: In your test ipynb file [see https://github.com/ma-compbio/Higashi/blob/main/tutorials/4DN_sci-Hi-C_Kim%20et%20al.ipynb], i have some question. 1, What is the label_info.pickle. I have data.txt but i don't know how to make the pickle file. 2, In the json,what is the data in the data_dir and temp_dir.

Thank you for your reply.

ruochiz commented 1 year ago

Hey, thanks for your interest.

  1. For label_info.pickle, see wiki page for more details: https://github.com/ma-compbio/Higashi/wiki/Input-Files
  2. within data_dir, there should be the data.txt and label_info.pickle. For temp_dir, Higashi would automatically creat some files like embeddings, imputations, etc. See more info here: https://github.com/ma-compbio/Higashi/wiki/Configure-the-parameters