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X3N1A authored Aug 27, 2024
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Expand Up @@ -113,7 +113,9 @@ $\dots$ input files in format: ```[<COOL_FILENAME>, <SHORT_NAME>]```

```"ChrNr": "15,16,17,18,19,20,21,22,X"``` $\dots$ chromosome numbers to be evaluated.

```"NormM": 0``` $\dots$ input contact matrices can be balanced. If ```NormM: 1```, balancing weights in cooler are applied. If set to 1, ENT3C expects weights to be in dataset ```/resolutions/<resolution>/bins/weight```.
```"NormM": 0``` $\dots$ input contact matrices can be balanced. If ```NormM: 1```, balancing weights in cooler are applied. If set to 1, ENT3C expects weights to be in dataset ```/resolutions/<resolution>/bins/<WEIGHTS_NAME>```.

```"WEIGHTS_NAME": "weight"``` $\dots$ name of dataset in cooler containing normalization weights.

```"SUB_M_SIZE_FIX": null``` $\dots$ fixed submatrix dimension.

Expand All @@ -126,7 +128,7 @@ If set, $\varphi$ is increased until $\Phi \approx \Phi\_{\max}$.

# Running main scripts
* ```julia ENT3C.jl --config-file=config/config.test.json --install-deps=no```
* ```matlab -nodesktop -nosplash -nodisplay -r "ENT3C; exit"```
* ```matlab -nodesktop -nosplash -nodisplay -r "ENT3C('config/config.test.json'); exit"```

Associated functions are contained in directories ```JULIA_functions/``` and ```MATLAB_functions/```.

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