https://github.com/hanjunlee21/hicshuffle

FASTQ Shuffling Tool For Sanity Check in Hi-C Differential Contact Analysis
https://github.com/hanjunlee21/hicshuffle

Last synced: 4 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 (over 3 years ago)
• Default Branch: main
• Last Pushed: 2023-12-08T21:49:14.000Z (over 1 year ago)
• Last Synced: 2025-02-24T23:07:40.805Z (5 months ago)
• Language: Python
• Size: 38.1 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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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 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

```