SSc ATAC-seq
The Python Code for the analysis of bulk ATAC-seq data of SSc patients and healthy controls
1. Requirement
We analyzed the scRNA-seq data in a Linux system with Python (version 2.7),R (version 3.5) enviroment. The following software and packages are also required:
| software | version | enviroment |
|---|---|---|
| ATAC-pipe | - | Linux |
| samtools | 1.9 | Linux |
| bedtools | 2.26.0 | Linux |
| bowtie2 | 2.3.0 | Linux |
| macs2 | 2.1.1 | Linux |
| picard | 2.9.2 | Linux |
| homer | 4.9.0 | Linux |
| numpy | 1.11.0 | python |
| pysam | 0.11 | python |
| matplotlib | 2.0.2 | python |
| pandas | 0.20.3 | python |
| seaborn | 0.9.1 | python |
| scipy | 0.19.1 | python |
| circlize | - | R |
2. Installation
Users need to copy the scripts to the same path as the "SourceData" folder.
3. Analysis
Users can run these scripts in Jupyter notebook directly, and get the figures of our paper.