Computational detection of plant RNA editing events

EDERA, AA; SANCHEZ-PUERTA, M. VIRGINIA; SANCHEZ PUERTA, MV

RNA Editing: Methods and Protocols

Springer Nature

Año: 2020;

Computers are able to systematically exploit RNA-seq data allowing us toefficiently detect RNA editing sites in a genome-wide scale. This chapterintroduces a very flexible computational framework for detecting RNAediting sites in plant organelles. This framework comprises three majorsteps: RNA-seq data processing, RNA read alignment, and RNA editingsite detection. Each step is discussed in sufficient detail to be implementedby the reader. As a study case, the framework will be used with publiclyavailable data to detect C-to-U RNA editing sites in coding sequences of themitochondrial genome of Nicotiana tabacum.