Local Methylation Profile Analysis

Overview

• Always prompt user for which columns in the BED files are methylation fraction/percent. Never decide by yourself.
• Generat profile: Bin methylation around regions (±flank, fixed bin size), aggregate mean±SE.
• Visualize: Plot mean profile with ribbon and center line.

---

Inputs & Outputs

Inputs

methylation.bed
target_regions.bed

Outputs

local_methyl_profile/
  stats/
    CpG_around_target.tsv
  plots/
    CpG_around_target.pdf
  temp/
    ... # other temp file generated

---

Decision Tree

Step 1: Preprocess input → 5-column BED (for methylKit), and 3-column BED (for target regions)

awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $2, $3, $<i_methylation>}, $<i_coverage>}' methylation.bed # n is provide by user, *100 if is fraction 
awk -F'\t' 'BEGIN {OFS="\t"} {print $1, $2, $3}' target_regions.bed

---

Step 2: Build methylation profiles around regions

Call:

• mcp__methyl-tools__build_local_methylation_profile

with:

• methyl_bed_path: 5-column BED-like file from preprocess_methylation.
• regions_bed_path: 3-column BED-like file from preprocess_regions.
• output_profile_tsv_path: path for aggregated profile table (TSV).
• flank_size: flank size in bp around region center (default 2000).
• bin_size: bin size in bp (default 50).
• min_coverage: minimum coverage threshold for CpGs (default 10).

---

Step 3: Visualization

Call:

• mcp__methyl-tools__plot_profile

with:

• profile_tsv_path: TSV from build_methylation_profile.
• output_plot_path: output figure path (PNG/PDF; format inferred from extension).
• title: plot title (optional).

---

Parameter Guidelines

| Context | Flank | Bin | Min cov | |-----------|-------|------|---------| | TF peaks | ±2 kb | 50bp | 10x | | Promoters | ±1 kb | 50bp | 10x | | Enhancers | ±5 kb | 100bp| 5x | | Motifs | ±0.5kb| 10–20| 10x |

Notes

• Snippets are usage hints and must be adapted to your paths and column indices.