tools-only Motif Analysis - Usage Guide
Overview
Identify DNA sequence motifs enriched in ChIP-seq or ATAC-seq peaks to reveal transcription factor binding sites and regulatory elements.
Prerequisites
# HOMER
conda install -c bioconda homer
perl /path/to/homer/configureHomer.pl -install hg38
# MEME Suite
conda install -c bioconda meme
Quick Start
Tell your AI agent what you want to do:
- "Find enriched motifs in my ChIP-seq peaks"
- "Discover transcription factor binding sites in ATAC-seq peaks"
- "Identify co-binding factors from my peak regions"
Example Prompts
De Novo Discovery
"Run de novo motif discovery on my ChIP-seq peaks"
"Find novel motifs enriched in my ATAC-seq accessible regions"
Known Motif Enrichment
"Test which known TF motifs are enriched in my peaks"
"Check if my ChIP-seq peaks contain the expected CTCF motif"
Comparative Analysis
"Compare motif enrichment between gained and lost peaks"
"Find motifs specific to condition-specific peaks"
What the Agent Will Do
- Extract peak sequences from the genome using the peak BED file
- Run de novo motif discovery (HOMER or MEME) on peak sequences
- Scan peaks against known motif databases (JASPAR, HOCOMOCO)
- Calculate enrichment statistics and rank motifs by significance
- Generate motif logos and summary reports
- Identify biologically relevant TFs based on enriched motifs
Tips
- Use
-size 200in HOMER to focus on the peak summit region - P-value < 1e-10 indicates strong enrichment
- Target % should be much higher than background % for meaningful motifs
- If only repeat-like motifs appear, enable repeat masking
- Check that the expected TF motif ranks highly to validate ChIP quality