Integrate seqOutBias for enzymatic bias correction

[edmundmiller]

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