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

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

Wang Z1,2, Lian J2, Li Q3,4, Zhang P2, Zhou Y2, Zhan X2,5, Zhang G6,7.

Author information

1
School of Bioscience & Bioengineering, South China University of Technology, Guangzhou, 510006, China.
2
China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China.
3
China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China. liqiye@genomics.cn.
4
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Ă˜ster Voldgade 5-7, 1350, Copenhagen K, Denmark. liqiye@genomics.cn.
5
College of Life Science and Technology, Jinan University, Guangzhou, 510000, China.
6
China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China. zhanggj@genomics.cn.
7
Centre for Social Evolution, Department of Biology, University of Copenhagen, Universitetsparken 15, DK-2100, Copenhagen, Denmark. zhanggj@genomics.cn.

Abstract

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

PMID:
27538485
PMCID:
PMC4989487
DOI:
10.1186/s13742-016-0143-4
[Indexed for MEDLINE]
Free PMC Article

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