This repository contains code for the analyses from the article "Dynamic of broad H3K4me3 domains uncover an epigenetic switch between cell identity and cancer-related genes". The workflow is written as a Snakemake wokflow which processes raw files into a Bookdown report. Since some of the raw files come from the DAC-restricted Blueprint project, the whole analysis can not be reproduced without access to these files.
The workflow has been compiled on a Linux environment with conda installed, following these instructions:
git clone git@github.com:guillaumecharbonnier/mw-lib.git
git clone git@github.com:guillaumecharbonnier/mw-belhocine2021.git
mw-belhocine2021/src/bash/run_snakemake_bookdown.sh
The rulegaph, DAG and listing of all tasks may help giving an overview of the Snakemake workflow without having to dive into the code.
Please open an issue on github if you have any questions.