usage-guide.md

CLIP Motif Analysis - Usage Guide

Overview

Find enriched sequence motifs at CLIP-seq binding sites to characterize RBP binding preferences.

Prerequisites

conda install -c bioconda homer meme bedtools

Quick Start

• "Find de novo motifs at binding sites"
• "Check for known RBP motifs"

Example Prompts

"Run HOMER motif analysis on my CLIP peaks"

"Find enriched 6-8mer motifs"

What the Agent Will Do

1. Extract peak sequences (bedtools getfasta)
2. Run de novo motif discovery
3. Compare to known RBP motifs
4. Report enriched motifs

Tips

• Use -rna flag for RNA motifs in HOMER
• Background should match GC content
• 6-8 nt motifs are typical for RBPs