usage-guide.md

Modification Visualization - Usage Guide

Overview

Visualize RNA modification patterns with metagene plots, heatmaps, and browser tracks.

Prerequisites

BiocManager::install(c('Guitar', 'TxDb.Hsapiens.UCSC.hg38.knownGene', 'ComplexHeatmap'))

conda install -c bioconda deeptools ucsc-bedtobigbed

Quick Start

• "Create metagene plot of m6A around stop codons"
• "Make browser tracks from my MeRIP data"
• "Visualize m6A distribution across transcripts"

Example Prompts

Metagene Plots

"Plot m6A distribution relative to UTRs and CDS"

"Create Guitar metagene plot from my peaks"

Browser Tracks

"Generate bigWig tracks for IGV"

"Make normalized coverage tracks from IP and input"

Heatmaps

"Create heatmap of m6A signal around peak centers"

"Cluster m6A peaks by signal pattern"

What the Agent Will Do

1. Load m6A peaks or signal data
2. Generate metagene profile around features
3. Create normalized browser tracks
4. Build signal heatmaps if requested
5. Export publication-ready figures

Tips

• Guitar - Best for transcript-centric metagene plots
• deepTools - Flexible for custom feature sets
• Stop codon enrichment - Classic m6A pattern (enriched near stop)
• Normalize - Use CPM or RPKM for comparable tracks
• IGV/UCSC - bigWig format for genome browsers