Using REDItools to Detect RNA Editing Events in NGS Datasets

Ernesto Picardi1, Anna Maria D'Erchia2, Antonio Montalvo3, Graziano Pesole1

1 National Institute of Biostructures and Biosystems (INBB), Rome, 2 Institute of Biomembranes and Bioenergetics, National Research Council, Bari, 3 University Hospital “Marqués de Valdecilla,” Santander
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 12.12
DOI:  10.1002/0471250953.bi1212s49
Online Posting Date:  March, 2015
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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. © 2015 by John Wiley & Sons, Inc.

Keywords: RNA editing; RNA‐Seq; DNA‐Seq; transcriptomics; NGS; next‐generation sequencing; REDItools

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: RNA Editing Detection Using RNA‐Seq and DNA‐Seq by REDItoolDnaRna.py
  • Support Protocol 1: Obtaining and Installing REDItools
  • Support Protocol 2: Preparing Input Files
  • Basic Protocol 2: Exploring RNA Editing in RNA‐Seq Data by REDItoolKnown.py
  • Basic Protocol 3: De Novo RNA Editing Detection Using RNA‐Seq Data Alone by REDItoolDenovo.py
  • Guidelines for Understanding Results
  • Commentary
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

Literature Cited
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Internet Resources
  http://code.google.com/p/reditools/
  Web site for downloading REDItools.
  http://150.145.82.212/ernesto/reditools/doc/
  REDItools online documentation.
  http://research‐pub.gene.com/gmap/
  Web site for downloading GSNAP program.
  http://www.python.org
  The official Python Web page.
  https://github.com/pysam‐developers/pysam
  Web site for downloading Pysam.
  https://pypi.python.org/pypi/fisher/
  Web site for downloading and installing the fisher module.
  http://hgdownload.cse.ucsc.edu/admin/exe/
  UCSC Web page for downloading Blat executables including gfServer and gfClient.
  http://en.wikipedia.org/wiki/FASTQ_format
  Wikipedia page describing the FASTQ format.
  http://samtools.github.io/hts‐specs/SAMv1.pdf
  SAM/BAM specifications.
  http://www.htslib.org/
  SAMtools Web page.
  http://picard.sourceforge.net/command‐line‐overview.shtml
  Picard tools for handling SAM/BAM files.
  http://rnaedit.com
  RADAR Web site comprising a compilation of known RNA editing in human, mouse and fly.
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