The Python Code for the analysis of bulk ATAC-seq data of SSc patients and healthy controls
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 |
Users need to copy the scripts to the same path as the "SourceData" folder.
Users can run these scripts in Jupyter notebook directly, and get the figures of our paper.