SKILL: Methylation Variability & Heterogeneity Analysis

Overview

Main steps include:

• Refer to the Inputs & Outputs section to check available inputs and design the output structure.
• Always prompt user for genome assembly used.
• Always prompt user for which columns in the BED files are methylation fraction/percent and coverage and strand.
• Building a multi-sample CpG methylation matrix from WGBS coverage files.
• Computing between-sample variability at CpG level (variance, MAD, CV).

When to use this skill

Use this methylKit-based variability pipeline when you want to: