Integrative Analysis of DNA Methylation and Chromatin Features

1. Overview

Main steps include:

• Refer to the Inputs & Outputs section to check required inputs and set up the output directory structure.
• Always prompt user for genome assembly used.
• Always prompt user for which columns in the methylation BED files are methylation fraction/percent and coverage and strand.
• Load and preprocess CpG methylation data
• Tile methylation into fixed-size windows (e.g., 1kb) or in target regions.
• Import chromatin feature signal from bigWig files
• Build a unified region-level integration table
• Calculate correlations between every two features.
• Visualization

2. When to Use This Skill