REDItools3 3.6

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REDItools3

A new REDItools implementation to speed-up the RNA editing profiling in massive RNAseq data

Installation

Install from PyPi. pip install REDItools3

Use the whl file under the dist directory. pip install dist/reditools-0.1-py3-none-any.whl

Usage

Once installed, reditools can be run from the commandline. python -m reditools

Tools

analyze

This is the core reditools function: detecting editing events from one or more BAM file.

The output is a tab separated table with these columns:

Field	Description
Region	Chromosome or contig
Position	Position in the region
Reference	Base from the reference sequence
Strand	DNA strand (+, -, or *)
Coverage	How many reads passed quality thresholds
MeanQ	Mean read quality
BaseCount[A,C,G,T]	Total count of each base found
AllSubs	All the detected substitutions
Frequency	Ratio of non-reference bases to reference bases
gCoverage	Genomic Coverage (see annotate)
gMeanQ	Genomic MeanQ (see annotate)
gBaseCount[A,C,G,T]	Genomic BaseCount (see annotate)
gAllSubs	Genomic variants (see annotate)
gFrequency	Genomic variant frequency (see annotate)

The last 5 columns will always be blank (-). They are reserved for output from the annotate tool.

annotate

Annotate RNA editing output with variant detection from genomic data.

annotate takes two reditools output files and fills in the last five columns of the first file with positional matches from the second.

For example, this RNA file:

Region	Position	Reference	Strand	Coverage	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
chr1	1115715	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
chr1	1115716	A	*	2	38.00	[2, 0, 0, 0]	-	0.00	-	-	-	-	-

With this DNA file:

Region	Position	Reference	Strand	Coverage	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
chr1	1115716	A	*	2	38.00	[2, 0, 0, 0]	-	0.00	-	-	-	-	-
chr1	1115717	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-

Produces:

Region	Position	Reference	Strand	Coverage	MeanQ	BaseCount[A,C,G,T]	AllSubs	Frequency	gCoverage	gMeanQ	gBaseCount[A,C,G,T]	gAllSubs	gFrequency
chr1	1115715	C	*	2	38.00	[0, 2, 0, 0]	-	0.00	-	-	-	-	-
chr1    1115716 A       *       2       38.00   [2, 0, 0, 0]    -       0.00    2       38.00   [2, 0, 0, 0]    -       0.00

find-repeats

Identify repetitive elements in a FASTQ file.

index

Compute RNA editing index from reditools analyze output (PMDI: 31636457). The index tool computes the editing indices for all possible variants, not just A-to-I (listed as A-G in the output).

Citing and Credit

Please cite the following papers when using REDItools3

1. Fonzino A, Mazzacuva PL, Handen A, Silvestris DA, Arnold A, Pecori R, Pesole G, Picardi E. REDInet: a temporal convolutional network-based classifier for A-to-I RNA editing detection harnessing million known events. Brief Bioinform. 2025 Mar 4;26(2):bbaf107. doi: 10.1093/bib/bbaf107. PMID: 40112338; PMCID: PMC11924403.
2. Picardi E, Pesole G. REDItools: high-throughput RNA editing detection made easy. Bioinformatics. 2013 Jul 15;29(14):1813-4. doi: 10.1093/bioinformatics/btt287. Epub 2013 Jun 5. PMID: 23742983.