Hyper_editing scripts Hyper_editing scripts for detection of hyper editing in RNA-Seq datasets

Introduction

Adenosine-to-inosine (Ato-I) editing is the most common form of editing in mammals,
and is catalysed by the adenosine deaminases ADAR1 and ADAR2 proteins.  ADAR tends to edit sites in clusters (‘hyper-editing’), current methods miss the heavily edited short reads.

This approach overcomes this obstacle (by pre-masking potential A-to-G-editing sites in unaligned reads) and enables the large-scale detection of hyper-edited reads in RNA-seq studies.

The pipeline includes four step: (1) collect all unmapped reads from the initial alignment; (2) transform all As to Gs in both the unmapped reads and the reference genome; (3) realign the transformed RNA reads and the transformed reference genome; and (4) recover the original sequences and search for dense clusters of A-to-G mismatches.

Publications

  1. A genome-wide map of hyper-edited RNA reveals numerous new sites
    Porath HT, Carmi S, Levanon EY, 2014 Aug 27 - Nature Communication
    Cited by Porath HT, Carmi S, Levanon EY. A genome-wide map of hyper-edited RNA reveals numerous new sites. Nat Commun. 2014 Aug 27;5:4726. doi: 10.1038/ncomms5726. PubMed PMID: 25158696; PubMed Central PMCID: PMC4365171. (Google Schoolar as of September 5, 2017)

Credits

  1. Hagit T. Porath Erez.Levanon@biu.ac.il
    Developer

    The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Israel

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Summary
AccessionBT007066
Tool TypePipeline & Protocol
CategoryRNA editing
PlatformsLinux/Unix, MAC OS X
TechnologiesBASH, Perl
User InterfaceTerminal Command Line
Input DataFASTQ
Latest Releasehypereditingscripts1.0 (September 4, 2017)
Download Count2542
Submitted Byli man