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Update readme.md
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cchlanger authored Jun 15, 2020
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Expand Up @@ -3,7 +3,7 @@ cooler_ontad is a tool that wraps [OnTAD](https://github.com/anlin00007/OnTAD) t
https://github.com/mirnylab/cooler).

This tool consists of three steps:
- It creates a dense matrix for OnTAD out of a mcooler file,
- It creates a dense matrix for OnTAD out of a .mcooler file,
- runs OnTAD,
- and creates a .bedpe out of the ONTAD results, all parameters used will be extended to the filename.

Expand All @@ -13,6 +13,8 @@ pip install ${githubpath}
This will set up a command called cooler_ontad in your environment.

## Usage Examples:
Example files can be found on [GEO](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE152373). You will need to [zoomify](https://github.com/mirnylab/cooler) .cooler to .mcooler first.

This will show all possible options, the tools support all options of OnTAD:

```cooler_ontad --help```
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