https://github.com/songlab-cal/hidensec
Code for Tracing cancer evolution and heterogeneity using Hi-C
https://github.com/songlab-cal/hidensec
Last synced: 22 days ago
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Code for Tracing cancer evolution and heterogeneity using Hi-C
- Host: GitHub
- URL: https://github.com/songlab-cal/hidensec
- Owner: songlab-cal
- Created: 2023-09-03T22:05:54.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-09-04T06:04:49.000Z (over 1 year ago)
- Last Synced: 2023-09-04T20:42:48.478Z (over 1 year ago)
- Language: Jupyter Notebook
- Size: 4.09 MB
- Stars: 0
- Watchers: 4
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# HiDENSEC: Code for Tracing cancer evolution and heterogeneity using Hi-C
Given a .hic file, in order to prepare it for running HiDENSEC, run the following command:
```
java -jar juicer_tools.jar dump observed NONE assembly assembly BP 25000 | tail -n+2 | awk -F $"\t" '{print $1*2"\t"$2*2"\t"$3}' | awk -F $"\t" '{print (($1/50000)+1)"\t"(($2/50000)+1)"\t"$3}' >
```
Here, `INPUT.hic` is the Hi-C file which can be generated using `https://github.com/aidenlab/juicer`.
The `OUTPUT.hi-c_matrix` is the output file name which will then be fed into the HiDENSEC jupyter notebook.
The `juicer_tools.jar` can be downloaded from `https://github.com/aidenlab/juicer/wiki/Download`