Reditools1

Introduction

REDItools v1.3 is a suite of Python scripts for detecting RNA editing events from RNA-seq data (and optionally matched DNA-seq). It supports de novo detection, DNA/RNA-paired calling, and known-site re-quantification, plus a set of table/GFF accessory utilities used to filter, annotate, sort, and index editing call tables. This module runs the upstream tools inside an Apptainer/Singularity image built from a Python 2.7 conda environment (pysam 0.15.4, samtools/htslib 1.9, numpy 1.16.6, scipy 1.2.3, fisher 0.1.5). Exposed commands Core callers (main/): REDItoolDenovo.py REDItoolDnaRna.py REDItoolKnown.py Nature Protocol runtime tools (NPscripts/): REDItoolDnaRnav13.py collect_editing_candidates.py get_Statistics.py Accessory utilities (accessory/): AnnotateTable.py FilterTable.py GFFtoTabix.py SearchInTable.py SortGFF.py SortTable.py TableToGFF.py get_DE_events.py readPsl.py rediportal2recoding.py selectPositions.py subCount.py subCount2.py tableToTabix.py Note: invoke each script with its full name including the .py suffix (e.g. “REDItoolDenovo.py -h”). The script’s own current directory is bound into the container, so input/output paths work as on the host. Citations - Picardi E, Pesole G. REDItools: high-throughput RNA editing detection made easy. Bioinformatics. 2013;29(14):1813-1814. - Lo Giudice C, Tangaro MA, Pesole G, Picardi E. Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal. Nat Protoc. 2020;15(3):1098-1131.

For more information, please check:
Home page: https://github.com/BioinfoUNIBA/REDItools
Documentation: https://github.com/BioinfoUNIBA/REDItools/blob/master/README_1.md
REDIportal: http://srv00.recas.ba.infn.it/atlas/

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

GAUTSCHI

1.3

NEGISHI

1.3

Commands

  • –

  • main/

  • (core

  • callers)

  • REDItoolDenovo.py

  • REDItoolDnaRna.py

  • REDItoolKnown.py

  • –

  • NPscripts/

  • (Nature

  • Protocol

  • runtime

  • tools

  • symlinked

  • into

  • /opt/REDItools/bin)

  • REDItoolDnaRnav13.py

  • collect_editing_candidates.py

  • get_Statistics.py

  • –

  • accessory/

  • (table

  • and

  • GFF

  • utilities)

  • AnnotateTable.py

  • FilterTable.py

  • GFFtoTabix.py

  • SearchInTable.py

  • SortGFF.py

  • SortTable.py

  • TableToGFF.py

  • get_DE_events.py

  • readPsl.py

  • rediportal2recoding.py

  • selectPositions.py

  • subCount.py

  • subCount2.py

  • tableToTabix.py

Module

You can load the modules by:

module load biocontainers
module load reditools1

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run reditools1 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -p wholenode        # Partition name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=reditools1
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers reditools1

# Your reditools1 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=reditools1
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers reditools1

# Your reditools1 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=reditools1
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers reditools1

# Your reditools1 workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=reditools1
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers reditools1

# Your reditools1 workflow...

#!/bin/bash
#SBATCH -A queue     # Queue name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=reditools1
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
module biocontainers reditools1

# Your reditools1 workflow...