Implement RNA degradation ratio calculation
Open
@edmundmiller is already working on this.
Since Jul 13, 2025.
enhancement
high-priority
- Dominant language
- Nextflow
- Stars
- 25
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
Description
Summary
Add PEPPRO's RNA degradation ratio metric for assessing RNA sample integrity.
Features to implement
- Insert size distribution calculation (single-end and paired-end)
- Degradation ratio: (10-20nt fragments) / (30-40nt fragments)
- Flash integration for paired-end overlap detection
- Insert size distribution plotting
Implementation details
- Create modules/local/rna_integrity
- Use cutadapt output for single-end calculations
- Integrate flash for paired-end fusion
- Generate insert size distribution plots
Technical specifications
- Target degradation ratio: <1.0 for high-quality libraries
- Support both single-end and paired-end data uniformly
- Account for UMI length in calculations
Acceptance criteria
- Degradation ratio calculation for both data types
- Insert size distribution plots
- Integration with QC reporting
- Proper UMI length accounting
References
- PEPPRO RNA integrity methods
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Assessment
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