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.
- 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)
- 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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