REDItools: python scripts for RNA editing detection by RNA-Seq data

Introduction

RNA editing is a post-transcriptional phenomenon involving the insertion/deletion or substitution of specific bases in precise RNA localizations. In humans, RNA editing occurs by deamination of cytosine to uridine (C-to-U) or mostly by the adenosine to inosine (A-to-I) conversion through ADAR enzymes. A-to-I substitutions may have profound functional consequences and have been linked to a variety of human diseases including neurological and neurodegenerative disorders or cancer. Next-generation sequencing technologies offer the unique opportunity to investigate in-depth RNA editing even though no dedicated software has been released up to now.

REDItools are simple Python scripts conceived to facilitate the investigation of RNA editing at large scale and devoted to research groups that would explore such phenomena in own data but don’t have sufficient bioinformatics skills. They work on main operating systems (although unix/linux-based OS are preferred), can handle reads from whatever platform in the standard BAM format, and implement various filters.

REDItools V1 manual

REDItools V2 manual

REDItools V3 manual

Note. REDItools V2 is useful for HPC environments.

REDItools V3 is the latest optimized version for large-scale investigations.

Important. Reditool_DNA_RNA.py v1.3 available at this link

Shield:

This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

This work is licensed under the Creative Commons Attribution - Non-Commercial 4.0 International License (CC BY-NC 4.0). For any commercial use or license request for market activities, interested parties are invited to contact the Technology Transfer Office (TTO) of the University of Bari Aldo Moro, copyright holder. For a copy of the license, please visit https://creativecommons.org/licenses/by-nc/4.0/