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Protocols

REDItools specifications

Information


Unique identifier OMICS_05860
Name REDItools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data BAM
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux, Mac OS
Programming languages Python
License BSD 3-clause “New” or “Revised” License, MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainers


  • person_outline Graziano Pesole
  • person_outline Ernesto Picardi

Publication for REDItools

REDItools citations

 (19)
library_books

Increased RNA Editing May Provide a Source for Autoantigens in Systemic Lupus Erythematosus

2018
Cell Rep
PMCID: 5905401
PMID: 29617672
DOI: 10.1016/j.celrep.2018.03.036

[…] RNA editing levels for a list of pre-known editing sites were calculated using REDIToolKnown, which is part of the REDItools package (). The list of editing sites was compiled from previous studies (, , ). […]

library_books

Whole transcriptome profiling of Late Onset Alzheimer’s Disease patients provides insights into the molecular changes involved in the disease

2018
Sci Rep
PMCID: 5844946
PMID: 29523845
DOI: 10.1038/s41598-018-22701-2

[…] RNA editing candidates were detected using REDItools. The Alu editing index, the weighted average editing level across all expressed Alu sequences, was calculated using custom scripts and according to the methodology described in Bazak et al.. […]

library_books

A to I RNA editing in the rat brain is age dependent, region specific and sensitive to environmental stress across generations

2018
BMC Genomics
PMCID: 5759210
PMID: 29310578
DOI: 10.1186/s12864-017-4409-8

[…] m/). Another method of mapping that counted and estimated proportions of A/G/T/C nucleotides (nucleotide pileup) at each edited site separately was used. Fastq reads were mapped using REDItoolDenovo (REDItools toolkit; []), against a single reference sequence in which the 5 edited sites of Htr2c contained N nucleotide, and allowing <=6 mismatches in the alignment. The two independent methods had h […]

library_books

Human cancer tissues exhibit reduced A to I editing of miRNAs coupled with elevated editing of their targets

2017
Nucleic Acids Res
PMCID: 5758889
PMID: 29165639
DOI: 10.1093/nar/gkx1176

[…] wnloaded the human miRNA predicted targets by TargetScanHuman 7.1 (), and used ANNOVAR () to find editing sites that modifies these targets. We then calculated the editing levels of these sites using REDITools () script, trimming 6bp on both sides of the read. Statistical significance was evaluated using Wilcoxon signed-rank test, followed by FDR multiple testing correction. To find miRNA gain alt […]

library_books

Rewriting the transcriptome: adenosine to inosine RNA editing by ADARs

2017
Genome Biol
PMCID: 5663115
PMID: 29084589
DOI: 10.1186/s13059-017-1347-3

[…] ee reference [] for a detailed perspective on this topic). Several databases are publically available to assess and query RNA-editing sites across species, including RADAR [], DARNED [, ], and REDIbd/REDItools []. […]

library_books

Massive transcriptome sequencing of human spinal cord tissues provides new insights into motor neuron degeneration in ALS

2017
Sci Rep
PMCID: 5577269
PMID: 28855684
DOI: 10.1038/s41598-017-10488-7

[…] stics were calculated using the CollectRnaSeqMetrics tool of Picard package (https://broadinstitute.github.io/picard/index.html) (Table ). The sporadic disease nature of our samples was checked using REDItools, screening known ALS mutations from ALSoD database in aligned RNAseq data. Only positions showing a frequency variation higher than 0.1 and supported by more than 10 reads we taken into acco […]


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REDItools institution(s)
Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari,Bari, Italy; Institute of Biomembranes and Bioenergetics, National Research Council, University of Bari, Bari, Italy; Center of Excellence in Comparative Genomics, University of Bari, Bari, Italy
REDItools funding source(s)
Supported by the Italian Ministero dell’Istruzione, Universita` e Ricerca (MIUR): PRIN 2009 and 2010; Consiglio Nazionale delle Ricerche: Flagship Project Epigen, Medicina Personalizzata and Aging Program 2012- 2014 and by the Italian Ministry for Foreign Affairs (Italy-Israel actions).

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