tools-only 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
- Extract peak sequences (bedtools getfasta)
- Run de novo motif discovery
- Compare to known RBP motifs
- 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