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Local Methylation Profile Analysis
local-methylation-profile
This skill analyzes the local DNA methylation profiles around target genomic regions provide by user. Use this skill when you want to vasulize the average methylation profile around target regions (e.g. TSS, CTCF peak or other target regions).
SKILL.md
Full skill instructions
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.
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