RES-Scanner: a software package for genome-wide identification of RNA-editing sites

Gigascience. 2016 Aug 18;5(1):37. doi: 10.1186/s13742-016-0143-4.


Background: High-throughput sequencing (HTS) provides a powerful solution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to distinguish RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors.

Results: Here we present RES-Scanner, a flexible and efficient software package that detects and annotates RNA-editing sites using matching RNA-seq and DNA-seq data from the same individuals or samples. RES-Scanner allows the use of both raw HTS reads and pre-aligned reads in BAM format as inputs. When inputs are HTS reads, RES-Scanner can invoke the BWA mapper to align reads to the reference genome automatically. To rigorously identify potential false positives resulting from genetic variants, we have equipped RES-Scanner with sophisticated statistical models to infer the reliability of homozygous genotypes called from DNA-seq data. These models are applicable to samples from either single individuals or a pool of multiple individuals if the ploidy information is known. In addition, RES-Scanner implements statistical tests to distinguish genuine RNA-editing sites from sequencing errors, and provides a series of sophisticated filtering options to remove false positives resulting from mapping errors. Finally, RES-Scanner can improve the completeness and accuracy of editing site identification when the data of multiple samples are available.

Conclusion: RES-Scanner, as a software package written in the Perl programming language, provides a comprehensive solution that addresses read mapping, homozygous genotype calling, de novo RNA-editing site identification and annotation for any species with matching RNA-seq and DNA-seq data. The package is freely available.

Keywords: Detection; Genome-wide; Identification; RES-Scanner; RNA editing; Software package.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods
  • High-Throughput Nucleotide Sequencing / methods*
  • Molecular Sequence Annotation
  • Programming Languages
  • RNA Editing*
  • Sequence Analysis, RNA / methods*
  • Software