wbaopaul/scatac-pro repository overview

scATAC-pro is an comprehensive pipeline for processing, analyzing and visualizing single cell chromatin accessibility data

⁠Input

• A test file configure_user.txt specifying options and parameters for each modules.

• A module name

• Each module needs a input file

• Recommend running the docker version through Singularity, see GitHub⁠ for more usage information

⁠Run in Docker

1. Install docker, and in your terminal:

2. $ docker run -dit -P --memory=10g --name test_scATAC-pro -v YOUR_WORK_DIR:/software wbaopaul/scatac-pro:latest

   • By this, your input and output data will be obtained and saved under YOUR_WORK_DIR, and you can change test_scATAC-pro to whatever name you like

3. $ docker attach test_scATAC-pro

4. $ scATAC-pro --help

⁠Output

All the output result will be saved under YOUR_WORK_DIR/output

⁠Citation

The detailed information is described in the following paper:

Yu, W., Uzun, Y., Zhu, Q., Chen, C., & Tan, K. (2020). scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data⁠. Genome Biology; 2020