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https://github.com/hanjunlee21/hicshuffle
FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis
https://github.com/hanjunlee21/hicshuffle
Last synced: about 2 months ago
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FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis
- Host: GitHub
- URL: https://github.com/hanjunlee21/hicshuffle
- Owner: hanjunlee21
- License: mit
- Created: 2022-02-07T07:52:42.000Z (almost 3 years ago)
- Default Branch: main
- Last Pushed: 2023-12-08T21:49:14.000Z (about 1 year ago)
- Last Synced: 2024-11-02T21:23:40.015Z (3 months ago)
- Language: Python
- Size: 38.1 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# HiCShuffle
[![PyPI version](https://badge.fury.io/py/HiCShuffle.svg)](https://badge.fury.io/py/HiCShuffle)
[![DOI:10.1101/2021.09.23.459925](https://zenodo.org/badge/DOI/10.1101/2021.09.23.459925.svg)](https://doi.org/10.1101/2021.09.23.459925)
[![MIT license](https://img.shields.io/badge/License-MIT-blue.svg)](https://lbesson.mit-license.org/)**FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis**
![HiCShuffle](https://hanjun.group/wp-content/uploads/2022/02/Extended-Data-Figure-X-01.png)
## Installation
```shell
pip install hicshuffle
```## Usage
### hicshuffle [options]
```shell
Commands:
diff FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis
Run hicshuffle -h for help on a specific command.HiCShuffle: FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis
positional arguments:
command Subcommand to runoptional arguments:
-h, --help show this help message and exit
--version show program's version number and exit
```### hicshuffle diff [-h] query_path_1 query_path_2 reference_path_1 reference_path_2 output_directory
```shell
FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis
positional arguments:
query_path_1 Path for READ1 of GZ-Compressed or Uncompressed Query FASTQ
query_path_2 Path for READ2 of GZ-Compressed or Uncompressed Query FASTQ
reference_path_1 Path for READ1 of GZ-Compressed or Uncompressed Reference FASTQ
reference_path_2 Path for READ2 of GZ-Compressed or Uncompressed Reference FASTQ
output_directory Output Directory... HiCShuffle Will Generate Output Directory If Not Existentoptional arguments:
-h, --help show this help message and exit
```