Add comprehensive nascent RNA QC metrics module
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@edmundmiller is already working on this.
Since Jul 13, 2025.
enhancement
- Dominant language
- Nextflow
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Description
Summary
Implement PEPPRO's comprehensive QC metrics for nascent RNA data quality assessment.
Features to implement
- Adapter-adapter ligation ratio calculation (target: 20-50% for non-size-selected)
- RNA degradation ratio (10-20nt vs 30-40nt fragments, target: <1.0)
- UMI-based library complexity assessment (target: ≥75% unique at 10M depth)
- Nascent RNA purity via exon-intron ratio (target: 1.0-1.8, excluding first exon)
- Run-on efficiency via pause index calculation (target: >10)
Implementation details
- Create new local module: modules/local/nascent_qc_metrics
- Add QC metrics to MultiQC custom content
- Generate JSON output for downstream processing
- Include threshold-based pass/fail recommendations
Acceptance criteria
- All 5 QC metrics implemented and tested
- Integration with existing MultiQC reports
- Configurable thresholds via params
- Comprehensive test coverage with test data
References
- PEPPRO paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02349-4
- Source implementation for reference
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