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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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>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.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>FLARE is a fast and flexible workflow that identifies significantly edited regions from RNA-seq data. The FLARE codebase is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/YeoLab\/FLARE\">https:\/\/github.com\/YeoLab\/FLARE<\/jats:ext-link>.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-023-05452-4","type":"journal-article","created":{"date-parts":[[2023,10,2]],"date-time":"2023-10-02T09:02:02Z","timestamp":1696237322000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["FLARE: a fast and flexible workflow for identifying RNA editing foci"],"prefix":"10.1186","volume":"24","author":[{"given":"Eric","family":"Kofman","sequence":"first","affiliation":[]},{"given":"Brian","family":"Yee","sequence":"additional","affiliation":[]},{"given":"Hugo C.","family":"Medina-Munoz","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0799-6037","authenticated-orcid":false,"given":"Gene W.","family":"Yeo","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,10,2]]},"reference":[{"issue":"3","key":"5452_CR1","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1101\/gr.164749.113","volume":"24","author":"L Bazak","year":"2014","unstructured":"Bazak L, Haviv A, Barak M, Jacob-Hirsch J, Deng P, Zhang R, Isaacs FJ, Rechavi G, Li JB, Eisenberg E, Levanon EY. 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The terms of these arrangements have been reviewed and approved by University of California San Diego in accordance with its conflict-of-interest policies. The authors declare no other competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"370"}}