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

Dataset type: Software
Data released on August 17, 2016

Li Q; Lian J; Wang Z; Zhan X; Zhang G; Zhang P; Zhou Y (2016): Software and supporting material for: "RES-Scanner: a software package for genome-wide identification of RNA-editing sites" GigaScience Database. http://dx.doi.org/10.5524/100211

DOI10.5524/100211

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.
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.
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

Additional details

Read the peer-reviewed publication(s):

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). doi:10.1186/s13742-016-0143-4

Related datasets:

doi:10.5524/100211 Cites doi:10.5524/100011

Additional information:

https://github.com/ZhangLabSZ/RES-Scanner





Funding body Awardee Award ID Comments
National Natural Science Foundation of China 31271392 G Zhang
National Natural Science Foundation of China 31501057 G Zhang
EU Marie Curie International Incoming Fellowship 300837
Date Action
August 17, 2016 Dataset publish
August 23, 2016 Manuscript Link added : 10.1186/s13742-016-0143-4