Repository of reproducible code for DOT1L project

This repository is a collection of jupyter notebooks and custom python scripts used in the analysis presented in the paper: "DOT1L Methyltransferase Activity Preserves SOX2-Enhancer Accessibility And Prevents Activation of Repressed Genes In Murine Stem Cells".

Setting up the environment for reproducing the results

1. Recreate the conda environments in your local machine. You find the requirements in the conda_environment folder;
2. Add the folder AUXILIARY_SCRIPTS to both your PATH variable and to your PYTHONPATH variable;
3. Install snakePipes v.1.1.1 (to do that, follow the detailed explanation available at https://snakepipes.readthedocs.io/en/latest/content/setting_up.html)

Workflow

1. Download the fastq files from GEO: GSE135318
2. Run the appropriate snakepipes pipelines to recreate the standard output folder structure.
3. After changing the paths according to your local file system, run the notebooks.