GSE215252
GSE GEO Potentially relatedFLARE: A fast and flexible peak-calling pipeline for identifying RNA editing foci
Relations
Summary
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 âlabelâ 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.
Overall Design
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.
Analysis (5 steps)
View Data Processing- STAR aligned original fastqs to hg19 reference build
- Run SAILOR to identify editing sites.
- Code available at: https://github.com/YeoLab/FLARE
- Run FLARE to identify regions of enriched editing.
- Code available at: https://github.com/YeoLab/FLARE
Supplementary Files (1)
GEO Samples (3)
Dataset Citations (1)
Potentially Related Publications (1)
This accession was text-mined from the PMC full text of these publications. It may be referenced for comparison or reused from another study rather than generated for them.
Data Files (3)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | RBFOX2_APO_rep1.fastqTr.sorted.STARUnmapped.out.sorted… | RNA-Seq | 145.6 MB | link | |||
| — | RBFOX2_APO_rep2.fastqTr.sorted.STARUnmapped.out.sorted… | RNA-Seq | 142.8 MB | link | |||
| — | RBFOX2_APO_rep3.fastqTr.sorted.STARUnmapped.out.sorted… | RNA-Seq | 98.0 MB | link |