FLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci

Experimental methods for discovering RNA Binding Protein (RBP) binding sites on target RNAs have recently emerged which employ fusions of RBPs to RNA-editing enzymes (such asAPOBEC1 or ADAR) to “label” mRNA. However, off-target editing, genetic variants and sequencing errors can lead to false positives when using data derived from such approaches, and highlight a need for a robust, statistical approach to prioritizing confident binding sites. Transiently transfected RBFOX2-APOBEC1 fusion construct expression was induced in HEK293 cells using doxycycline for 72 hours before samples were prepared for RNA sequencing. We present FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that uses a statistical approach to determine regions of enriched RNA editing, using SAILOR-derived editing sites as a starting point.