Summary

Implement NRSA's multi-factorial enhancer prioritization algorithm with advanced target gene assignment strategies.

Features to implement

• Multi-strategy target gene assignment (closest TSS, distance-based, FANTOM5, 4DGenome)
• Enhancer prioritization scoring combining binding affinity and functional activity
• Long eRNA detection (>10kb transcripts)
• Alternative TSS/TTS identification

Implementation details

• Create subworkflow: subworkflows/local/enhancer_analysis
• Implement multi-strategy gene assignment algorithm
• Add enhancer scoring and ranking system
• Generate specialized output files for enhancer centers

Technical specifications

• Default distance threshold: 50kb (configurable)
• Support FANTOM5 database integration
• Multi-factorial scoring system implementation
• BED format outputs for enhancer coordinates

Acceptance criteria

• Multi-strategy target gene assignment working
• Enhancer prioritization scoring implemented
• Long eRNA detection functional
• Integration with existing peak calling
• Comprehensive test coverage

References

• NRSA enhancer analysis: https://bioinfo.vanderbilt.edu/NRSA/