期刊
BRIEFINGS IN BIOINFORMATICS
卷 20, 期 2, 页码 436-447出版社
OXFORD UNIV PRESS
DOI: 10.1093/bib/bbx129
关键词
RNA editing; RNA-Seq; transcriptome; simulation; benchmark data set
资金
- Italian Ministero dell'Istruzione, Universita e Ricerca (MIUR): PRIN 2012
- Consiglio Nazionale delle Ricerche: Flagship Project Epigen
- Medicina Personalizzata
- Aging Program
- Interomics
- Elixir-IIB
RNA editing is a widespread co/posttranscriptional mechanism affecting primary RNAs by specific nucleotide modifications, which plays relevant roles in molecular processes including regulation of gene expression and/or the processing of noncoding RNAs. In recent years, the detection of editing sites has been improved through the availability of high-throughput RNA sequencing (RNA-Seq) technologies. Accurate bioinformatics pipelines are essential for the analysis of next-generation sequencing (NGS) data to ensure the correct identification of edited sites. Several pipelines, using various read mappers and variant callers with a wide range of adjustable parameters, are available for the detection of RNA editing events. In this review, we discuss some of the most recent and popular tools and provide guidelines for RNA-Seq data generation and analysis for the detection of RNA editing in massive transcriptome data. Using simulated and real data sets, we provide an overview of their behavior, emphasizing the fact that the RNA editing detection in NGS data sets remains a challenging task.
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