Software and supporting material for: "RES-Scanner: a software package for genome-wide identification of RNA-editing sites"

High-throughput sequencing (HTS) provides a powerful resolution for the genome-wide identification of RNA-editing sites. However, it remains a great challenge to discriminate RNA-editing sites from genetic variants and technical artifacts caused by sequencing or read-mapping errors.<br>
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 using both raw HTS reads and pre-aligned reads in BAM format as inputs. While inputs are HTS reads, RES-Scanner can invoke BWA to align reads to the reference genome automatically. To rigorously discriminate potential false positives resulted from genetic variants, we equip 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 both a single individual and a pool of multiple individuals given that the ploidy information is known. In addition, RES-Scanner implements statistical tests to discriminate genuine RNA-editing sites from sequencing error, and provides a series of sophisticated filtering options to remove false positives resulted from mapping errors. Finally, RES-Scanner can improve the completeness and accuracy of editing site identification when the data of multiple samples are available.<br>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 at: https://github.com/ZhangLabSZ/RES-Scanner