Assessment of transcript reconstruction methods for RNA-seq

Steijger, Tamara, Abril, Josep F., Engsrtom, Par G., Kokocinski, Felix, The RGASP Consortium, Hubbard, Tim J., Guigo, Roderic, Harrow, Jennifer, Bertone, Paul, Cloonan, Nicole and Grimmond, Sean (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 12: 1177-1186. doi:10.1038/nMeth.2714

Author Steijger, Tamara
Abril, Josep F.
Engsrtom, Par G.
Kokocinski, Felix
The RGASP Consortium
Hubbard, Tim J.
Guigo, Roderic
Harrow, Jennifer
Bertone, Paul
Cloonan, Nicole
Grimmond, Sean
Title Assessment of transcript reconstruction methods for RNA-seq
Journal name Nature Methods   Check publisher's open access policy
ISSN 1548-7091
Publication date 2013-12-01
Sub-type Article (original research)
DOI 10.1038/nMeth.2714
Open Access Status
Volume 10
Issue 12
Start page 1177
End page 1186
Total pages 10
Place of publication London, United Kingdom
Publisher Nature Publishing Group
Language eng
Subject 1305 Biotechnology
1303 Biochemistry
1312 Molecular Biology
1307 Cell Biology
Abstract We evaluated 25 protocol variants of 14 independent computational methods for exon identification, transcript reconstruction and expression-level quantification from RNA-seq data. Our results show that most algorithms are able to identify discrete transcript components with high success rates but that assembly of complete isoform structures poses a major challenge even when all constituent elements are identified. Expression-level estimates also varied widely across methods, even when based on similar transcript models. Consequently, the complexity of higher eukaryotic genomes imposes severe limitations on transcript recall and splice product discrimination that are likely to remain limiting factors for the analysis of current-generation RNA-seq data.
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID U54HG004555
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
Institute for Molecular Bioscience - Publications
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 169 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 171 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Tue, 10 Dec 2013, 20:24:24 EST by Susan Allen on behalf of Institute for Molecular Bioscience