Analysis and design of RNA sequencing experiments for identifying RNA editing and other single-nucleotide variants

RNA. 2013 Jun;19(6):725-32. doi: 10.1261/rna.037903.112. Epub 2013 Apr 18.


RNA-sequencing (RNA-Seq) technologies hold enormous promise for novel discoveries in genomics and transcriptomics. In the past year, a surge of reports has analyzed RNA-Seq data to gain a global view of the RNA editome. Opposing results have been presented, giving rise to extensive debate surrounding one of the first such studies in which a daunting list of all 12 types of RNA-DNA differences (RDDs) were identified. Although a consensus is forming that some of the initial "paradigm-shifting" results of this study may be questionable, recent reports on this topic differed in terms of the number and relative abundance of each type of RDD. Many outstanding issues exist, most importantly, the choice of bioinformatic approaches. Here we discuss the critical data analysis and experimental design issues of such studies to enable improved systematic investigation of the largely unexplored frontier of single-nucleotide variants in RNA.

Keywords: RNA editing; RNA-Seq; RNA–DNA difference; mapping error; read mapping.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Base Sequence
  • Databases, Nucleic Acid
  • Gene Expression Profiling / methods
  • Humans
  • Molecular Sequence Annotation
  • Polymorphism, Single Nucleotide*
  • RNA Editing*
  • RNA Splice Sites
  • Reproducibility of Results
  • Research Design*
  • Sensitivity and Specificity
  • Sequence Alignment
  • Sequence Analysis, RNA / methods*


  • RNA Splice Sites