Article (Scientific journals)
RNASEQR—a streamlined and accurate RNA-seq sequence analysis program
Chen, Leslie Y.; Wei, Kuo-Chen; Huang, Abner C.-Y. et al.
2012In Nucleic Acids Research, 40 (6), p. 42
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Abstract :
[en] Next-generation sequencing (NGS) technologiesbased transcriptomic profiling method often called RNA-seq has been widely used to study global gene expression, alternative exon usage, new exon discovery, novel transcriptional isoforms and genomic sequence variations. However, this technique also poses many biological and informatics challenges to extracting meaningful biological information. The RNA-seq data analysis is built on the foundation of high quality initial genome localization and alignment information for RNA-seq sequences. Toward this goal, we have developed RNASEQR to accurately and effectively map millions of RNA-seq sequences. We have systematically compared RNASEQR with four of the most widely used tools using a simulated data set created from the Consensus CDS project and two experimental RNA-seq data sets generated from a human glioblastoma patient. Our results showed that RNASEQR yields more accurate estimates for gene expression, complete gene structures and new transcript isoforms, as well as more accurate detection of single nucleotide variants (SNVs). RNASEQR analyzes raw data from RNA-seq experiments effectively and outputs results in a manner that is compatible with a wide variety of specialized downstream analyses on desktop computers.
Research center :
Luxembourg Centre for Systems Biomedicine (LCSB): Experimental Neurobiology (Balling Group)
Disciplines :
Life sciences: Multidisciplinary, general & others
Author, co-author :
Chen, Leslie Y.
Wei, Kuo-Chen
Huang, Abner C.-Y.
Wang, Kai
Huang, Chiung-Yin
Yi, Danielle
Tang, Chuan Yi
Galas, David J. ;  University of Luxembourg > Luxembourg Centre for Systems Biomedicine (LCSB)
Hood, Leroy E.
External co-authors :
yes
Language :
English
Title :
RNASEQR—a streamlined and accurate RNA-seq sequence analysis program
Publication date :
2012
Journal title :
Nucleic Acids Research
ISSN :
1362-4962
Publisher :
Oxford University Press, Oxford, United Kingdom
Volume :
40
Issue :
6
Pages :
e42-
Peer reviewed :
Peer Reviewed verified by ORBi
Available on ORBilu :
since 08 April 2016

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