title: Using REDItools to Detect RNA Editing Events in NGS Datasets.
abstract: RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts.
authors.affiliation: Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.|Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy.|National Institute of Biostructures and Biosystems (INBB), Rome, Italy.
authors.forename: Ernesto
authors.initials: E
authors.lastname: Picardi
authors.affiliation: Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.|Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy.
authors.forename: Anna Maria
authors.initials: AM
authors.lastname: D'Erchia
authors.affiliation: Department of Molecular Biology, Faculty of Medicine, University of Cantabria, Santander, Spain.|University Hospital "Marqués de Valdecilla," Santander, Spain.
authors.forename: Antonio
authors.initials: A
authors.lastname: Montalvo
authors.affiliation: Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy.|Institute of Biomembranes and Bioenergetics, National Research Council, Bari, Italy.|National Institute of Biostructures and Biosystems (INBB), Rome, Italy.
authors.forename: Graziano
authors.initials: G
authors.lastname: Pesole
mesh_terms: D030561:Databases, Nucleic Acid; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017393:RNA Editing / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA; D012984:Software
keywords: DNA-Seq; NGS; REDItools; RNA editing; RNA-Seq; next-generation sequencing; transcriptomics