FLARE: a fast and flexible workflow for identifying RNA editing foci
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 posit...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s12859-023-05452-4 |
| _version_ | 1827707947966267392 |
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| author | Eric Kofman Brian Yee Hugo C. Medina-Munoz Gene W. Yeo |
| author_facet | Eric Kofman Brian Yee Hugo C. Medina-Munoz Gene W. Yeo |
| author_sort | Eric Kofman |
| collection | DOAJ |
| description | 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 . |
| first_indexed | 2024-03-10T16:56:50Z |
| format | Article |
| id | doaj.art-60fd58a8fbc4499381f485d2f5c347e6 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-03-10T16:56:50Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-60fd58a8fbc4499381f485d2f5c347e62023-11-20T11:06:26ZengBMCBMC Bioinformatics1471-21052023-10-0124111510.1186/s12859-023-05452-4FLARE: a fast and flexible workflow for identifying RNA editing fociEric Kofman0Brian Yee1Hugo C. Medina-Munoz2Gene W. Yeo3Department of Cellular and Molecular Medicine, University of California San DiegoDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Cellular and Molecular Medicine, University of California San DiegoDepartment of Cellular and Molecular Medicine, University of California San DiegoAbstract 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 .https://doi.org/10.1186/s12859-023-05452-4RNA editingClusteringStatisticalModeling |
| spellingShingle | Eric Kofman Brian Yee Hugo C. Medina-Munoz Gene W. Yeo FLARE: a fast and flexible workflow for identifying RNA editing foci BMC Bioinformatics RNA editing Clustering Statistical Modeling |
| title | FLARE: a fast and flexible workflow for identifying RNA editing foci |
| title_full | FLARE: a fast and flexible workflow for identifying RNA editing foci |
| title_fullStr | FLARE: a fast and flexible workflow for identifying RNA editing foci |
| title_full_unstemmed | FLARE: a fast and flexible workflow for identifying RNA editing foci |
| title_short | FLARE: a fast and flexible workflow for identifying RNA editing foci |
| title_sort | flare a fast and flexible workflow for identifying rna editing foci |
| topic | RNA editing Clustering Statistical Modeling |
| url | https://doi.org/10.1186/s12859-023-05452-4 |
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