Integrate seqOutBias for enzymatic bias correction
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@edmundmiller is already working on this.
Since Jul 13, 2025.
- Dominant language
- Nextflow
- Stars
- 25
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
Description
Summary
Add optional seqOutBias integration for correcting T4 RNA Ligase and other enzymatic biases in nascent RNA data.
Features to implement
- Optional seqOutBias bias correction
- Tallymer index support for k-mer counting
- Bias-corrected bigWig generation
- Configurable k-mer length support
Implementation details
- Add seqOutBias to container/conda environment
- Create bias correction module with tallymer integration
- Make bias correction optional via params
- Generate both raw and bias-corrected tracks
Acceptance criteria
- seqOutBias integration working
- Tallymer index generation
- Optional bias correction parameter
- Both corrected and uncorrected outputs
- 15-20% improvement in peak calling accuracy
References
- PEPPRO bias correction implementation
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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