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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

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FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis

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# 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 run

optional 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 Existent

optional arguments:
-h, --help show this help message and exit
```