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

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.

Here researchers from the South China University of Technology 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, the researchers 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.

Overview of the workflow of RES-Scanner


RES-Scanner employs a three-part framework to detect RNA-editing sites with matching DNA-seq and RNA-seq data, including RNA/DNA-seq read mapping and filtering, homozygous genotype calling and identification of RNA-editing candidates

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.

Availability – The package is freely available at:

Wang Z, Lian J, Li Q, Zhang P, Zhou Y, Zhan X, Zhang G. (2016) RES-Scanner: a software package for genome-wide identification of RNA-editing sites. Gigascience 5(1):37. [article]

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