title: RES-Scanner: a software package for genome-wide identification of RNA-editing sites.
abstract: 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 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.
  
  
  
  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.
authors.affiliation: School of Bioscience & Bioengineering, South China University of Technology, Guangzhou, 510006, China.|China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Zongji
authors.initials: Z
authors.lastname: Wang
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Jinmin
authors.initials: J
authors.lastname: Lian
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China. liqiye@genomics.cn.|Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350, Copenhagen K, Denmark. liqiye@genomics.cn.
authors.forename: Qiye
authors.initials: Q
authors.lastname: Li
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Pei
authors.initials: P
authors.lastname: Zhang
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.|College of Life Science and Technology, Jinan University, Guangzhou, 510000, China.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhan
authors.affiliation: China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China. zhanggj@genomics.cn.|Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark. zhanggj@genomics.cn.
authors.forename: Guojie
authors.initials: G
authors.lastname: Zhang
mesh_terms: D019295:Computational Biology / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation; D011381:Programming Languages; D017393:RNA Editing; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
keywords: Detection; Genome-wide; Identification; RES-Scanner; RNA editing; Software package