FLARE: a fast and flexible workflow for identifying RNA editing foci

Area of Science:

• Molecular Biology
• Bioinformatics
• Genomics

Background:

• RNA-binding proteins (RBPs) fused to RNA base editors aid RBP binding site discovery.
• Existing methods suffer from false positives due to off-target editing, genetic variation, and sequencing errors.

Purpose of the Study:

• To develop a robust computational pipeline for identifying RNA editing sites.
• To improve the accuracy of RBP binding site discovery by minimizing false positives.

Main Methods:

• Developed FLARE (FLagging Areas of RNA-editing Enrichment), a Snakemake-based pipeline.
• FLARE processes outputs from the SAILOR edit site discovery tool.
• The pipeline is configurable for various RNA editing types (C-to-U, A-to-I).

Main Results:

• FLARE identifies regions statistically enriched for RNA editing.
• Applied to RBFOX2-APOBEC1 STAMP data, FLARE demonstrated high specificity for RBFOX2 binding sites.
• Successfully detected both exogenous and endogenous A-to-I editing regions.

Conclusions:

• FLARE provides a fast and flexible workflow for analyzing RNA-seq data to find significantly edited regions.
• The FLARE codebase is publicly available for research use.