usage-guide.md

CLIP Peak Calling - Usage Guide

Overview

Call protein-RNA binding site peaks from aligned CLIP-seq data.

Prerequisites

conda install -c bioconda clipper piranha pureclip

Quick Start

Tell your AI agent what you want to do:

• "Call peaks with CLIPper"
• "Run PureCLIP for HMM-based crosslink site detection"
• "Find significant binding clusters"
• "Call peaks with input control normalization"

Example Prompts

CLIPper

"Run CLIPper on my deduped BAM"

"Call peaks with FDR < 0.05"

PureCLIP

"Run PureCLIP for single-nucleotide crosslink detection"

"Call peaks with PureCLIP using my input control"

"Get high-confidence binding regions from eCLIP data"

What the Agent Will Do

1. Run peak caller (CLIPper, PureCLIP, or Piranha) on aligned BAM
2. Apply significance filtering (FDR, p-value, or score threshold)
3. Output BED files with peaks or crosslink sites
4. Calculate quality metrics (FRiP, peak count)

Tips

• CLIPper is ENCODE standard for eCLIP
• PureCLIP uses HMM for single-nucleotide crosslink site resolution
• Use deduplicated BAM for accurate calling
• Input control improves specificity (use with PureCLIP -ibam)
• Score filtering: PureCLIP score >= 3 for medium confidence, >= 5 for high