Dataset Information
FLARE: a fast and flexible workflow for identifying RNA editing foci.
Ontology highlight
ABSTRACT: Background
Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable to false positives due to off-target editing, genetic variation and sequencing errors.Results
We present FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that builds on the outputs of the SAILOR edit site discovery tool to identify regions statistically enriched for RNA editing. FLARE can be configured to analyze any type of RNA editing, including C to U and A to I. We applied FLARE to C-to-U editing data from a RBFOX2-APOBEC1 STAMP experiment, to show that our approach attains high specificity for detecting RBFOX2 binding sites. We also applied FLARE to detect regions of exogenously introduced as well as endogenous A-to-I editing.Conclusions
FLARE is a fast and flexible workflow that identifies significantly edited regions from RNA-seq data. The FLARE codebase is available at https://github.com/YeoLab/FLARE .
SUBMITTER: Kofman E
PROVIDER: S-EPMC10544219 | biostudies-literature | 2023 Oct
REPOSITORIES: biostudies-literature
Publications
FLARE: a fast and flexible workflow for identifying RNA editing foci.
BMC bioinformatics 20231002 1
<h4>Background</h4>Fusion of RNA-binding proteins (RBPs) to RNA base-editing enzymes (such as APOBEC1 or ADAR) has emerged as a powerful tool for the discovery of RBP binding sites. However, current methods that analyze sequencing data from RNA-base editing experiments are vulnerable to false positives due to off-target editing, genetic variation and sequencing errors.<h4>Results</h4>We present FLagging Areas of RNA-editing Enrichment (FLARE), a Snakemake-based pipeline that builds on the output ...[more]
