REDItools pipeline

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


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Documentation


Maintainers


  • person_outline Graziano Pesole <>
  • person_outline Ernesto Picardi <>

Publication for REDItools

REDItools IN pipelines

 (5)
2018
PMCID: 5844946
PMID: 29523845
DOI: 10.1038/s41598-018-22701-2

[…] experiments. statistical analysis was performed by two-tailed student’s t tests and a p-value < 0.05 was considered statistically significant., rna editing candidates were detected using reditools74. 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 […]

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

[…] level across all expressed alu sequences, was calculated using custom scripts and according to the methodology described in bazak et al.75. rna editing levels in recoding sites were assessed using reditools and providing a list of 1585 known positions from rediportal database37 in which rna editing causes amino acid change. only positions supported by rnaseq reads in at least three samples per […]

2015
PMCID: 4597103
PMID: 26501059
DOI: 10.3389/fbioe.2015.00156

[…] by picardi et al. (2014). they described a novel computational approach to reliably detect a-to-i editing events in human lncrnas through ngs, based on their previously published package called reditools. in the presented article, the authors showed the potential of their tools in recovering a-to-i candidates from rnaseq data and provided guidelines to improve rna editing detection […]

2014
PMCID: 4257104
PMID: 25538940
DOI: 10.3389/fbioe.2014.00064

[…] works accurately, misalignment errors may occur. the mismapping effect can be mitigated realigning reads carrying mismatches by the classical blat algorithm through an ad hoc script included in reditools (reditoolblatcorrection.py). such script identifies reads prone to mismapping and collects them in specific lists, ready to be inspected by main reditools programs., uncovering rna editing […]

2014
PMCID: 4257104
PMID: 25538940
DOI: 10.3389/fbioe.2014.00064

[…] through an ad hoc script included in reditools (reditoolblatcorrection.py). such script identifies reads prone to mismapping and collects them in specific lists, ready to be inspected by main reditools programs., uncovering rna editing in lncrnas is based on the reditooldnarna.py script in which single rna editing modifications are identified by comparing pre-aligned rna-seq and dna-seq […]

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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