REDItools protocols

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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

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Maintainers


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

Publication for REDItools

REDItools in pipelines

 (7)
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 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 […]

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

[…] this measurement results in a clean signal with a minimal false-positive rate ()., 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 (, , )., the deseq package () in r was used for analyzing differential gene expression in all control and sle […]

2017
PMCID: 5301482
PMID: 28186130
DOI: 10.1038/srep42250

[…] reads were extracted by samtools with the parameter ‘flag = 16’ to separate those mapped to the forward and reverse strands. finally, rna editing sites from both strands were separately called by reditools with the following cutoffs: coverage ≥ 5, frequency ≥ 0.1, and p ≤ 0.05. we named this approach the “mapping-based method”., given this mapping-based method, a critical parameter […]

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

[…] 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 […]

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

[…] als and healthy control patients as biological replicates. pathway analysis was conducted with mirpath v2.0 with default settings., rna editing candidates per each sample were detected using the reditools package (https://sourceforge.net/projects/reditools/). in particular, reditoolknown.py was used to explore known rna editing sites stored in rediportal database. non-metric multidimensional […]


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REDItools in publications

 (15)
PMCID: 5905401
PMID: 29617672
DOI: 10.1016/j.celrep.2018.03.036

[…] this measurement results in a clean signal with a minimal false-positive rate ()., 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 (, , )., the deseq package () in r was used for analyzing differential gene expression in all control and sle […]

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

[…] 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 […]

PMCID: 5758889
PMID: 29165639
DOI: 10.1093/nar/gkx1176

[…] 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 […]

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

[…] read is equal to the double of the number of fragments., to confirm the sporadic disease nature of our samples, we checked for the presence of known als mutations in aligned rnaseq data using reditools and did not find any potentially fals- associated variant in the causative genes annotated in the als online genetic database (alsod http://alsod.iop.kcl.ac.uk/)., we calculated rnaseq […]

PMCID: 5550009
PMID: 28746393
DOI: 10.1371/journal.pgen.1006931

[…] localize in specific position, suggesting sequence errors as a source for this bias (). therefore, non a-to-g mismatches were eliminated in this work., the analyses of editing levels were done using reditools script[], which systematically identifies rna editing events from a given list of sites. to reduce sequencing errors, six bases were trimmed out up and down the reads. we demanded […]


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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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