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Title: Software and supporting material for: "RES-Scanner: a software package for genome-wide identification of RNA-editing sites"      
dateReleased:
08-15-2016
privacy:
not applicable
aggregation:
instance of dataset
dateCreated:
08-15-2016
refinement:
curated
ID:
doi:10.5524/100211
creators:
,
Zhang, Pei
Zhou, Yang
availability:
available
types:
sequence
description:
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
accessURL: https://doi.org/10.5524/100211
storedIn:
GigaScience Database
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
GigaDB
homePage: http://gigadb.org/
ID:
SCR:006565
name:
Giga Science Database

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