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Update README.md
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pkerpedjiev authored Jul 10, 2018
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Expand Up @@ -53,34 +53,6 @@ curl http://localhost:8000/api/v1/tileset_info/?d=hitile-demo
curl http://localhost:8000/api/v1/tiles/?d=hitile-demo.0.0.0
```

## Preparing files for ingest

Genomics data needs to be aggregated across a range of scales before it can be used with HiGlass.

### Cooler files

**TODO**: Is this still accurate?

[Cooler](https://github.com/mirnylab/cooler) files store Hi-C data. They need to be decorated with aggregated
data at multiple resolutions in order to work with `higlass-server`. This is easily accomplished by simply
installing the `cooler` python package and running the `recursive_agg_onefile.py` script. For now this has
to come from a clone of the official cooler repository, but this will hopefully be merged into the main branch shortly.

```
git clone -b develop https://github.com/pkerpedjiev/cooler.git
cd cooler
python setup.py install
recursive_agg_onefile.py file.cooler --out output.cooler
```

### BigWig files

BigWig files can be aggregated with the [Clodius](https://github.com/hms-dbmi/clodius#bigwig-files).

### **TODO**: Any other types?

---

## Development
Expand Down Expand Up @@ -116,3 +88,7 @@ bumpversion patch
## Troubleshooting

**pybbi installation fails on macOS**: Check out https://github.com/nvictus/pybbi/issues/2

## License

The code in this repository is provided under the MIT License.

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