Unmethylated Regions (UMR) & Low-Methylated Region (LMR) & Partially Methylated Domain (PMD) Detection

1. Overview

This pipeline performs genome-wide segmentation of CpG methylation profiles to identify Unmethylated Regions (UMRs), Low-Methylated Regions (LMRs), and Partially Methylated Domains (PMDs) using whole-genome bisulfite sequencing (WGBS) methylation calls.

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 are methylation fraction/percent and coverage and strand.
• Convert BED → GRanges with mC/nC counts.
• Perform CpG filtering (coverage threshold).
• Call UMRs/LMRs using MethylSeekR segmentation.
• Mask UMR/LMR and detect PMDs using a 2-state HMM (optional).
• Export annotations as BED files and summary tables.

2. When to Use This Skill