Disentangling tumor- from age-associated DNA methylation changes occurring in the colonic mucosa of women

Code and data analysis

This repository contains the code for the following paper:

• S Orjuela, HR Parker, S Sajibu, F Cereatti, M Sauter, F Buffoli, MD Robinson and G Marra: Disentangling tumor- from age-associated DNA methylation changes occurring in the colonic mucosa of women.

All files outside the scripts/ folder are necessary to run a Snakemake workflow with:

snakemake --use-conda -cores 1 similar to the ARMOR pipeline

Before running the pipeline, raw FASTQ files must be downloaded from here (lesion females) and here (healthy females). The location of the FASTQ files must be specified in config.yaml. Please download the files from the "Submitted FTP" section, because the file names match the names in metadata_*.txt

Folder description:

• scripts/ R scripts with code for DMR detection analysis, and code for plotting most of figures in paper.
• data/ .RData objects with DMR lists mentioned in the publication.