Repository: Freie Universität Berlin, Math Department

Assessment of transcript reconstruction methods for RNA-seq

Steijger, T. and Abril, J. F. and Engström, P. G. and Kokocinski, F. and The RGASP Consortium, and Richard, H. and Schulz, M. H. and Weese, D. and Hubbard, T. and Guigó, R. and Harrow, J. and Bertone, P. (2013) Assessment of transcript reconstruction methods for RNA-seq. Nature Methods, 10 (12). pp. 1177-1184.

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Official URL: http://dx.doi.org/10.1038/nmeth.2714

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.

Item Type:Article
Subjects:Biological Sciences
Mathematical and Computer Sciences > Computer Science
Divisions:Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
ID Code:1380
Deposited By: AG Alg BioInf
Deposited On:20 Feb 2014 22:54
Last Modified:03 Mar 2017 14:41

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