title: Assessment of transcript reconstruction methods for RNA-seq.
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.
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
authors.forename: Tamara
authors.initials: T
authors.lastname: Steijger
authors.affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain.
authors.forename: Josep F
authors.initials: JF
authors.lastname: Abril
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.
authors.forename: Pär G
authors.initials: PG
authors.lastname: Engström
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Felix
authors.initials: F
authors.lastname: Kokocinski
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Tim J
authors.initials: TJ
authors.lastname: Hubbard
authors.affiliation: Center for Genomic Regulation, Barcelona, Spain.|Universitat Pompeu Fabra, Barcelona, Spain.
authors.forename: Roderic
authors.initials: R
authors.lastname: Guigó
authors.affiliation: Wellcome Trust Sanger Institute, Cambridge, UK.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Harrow
authors.affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK.|Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.|Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.|Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK.
authors.forename: Paul
authors.initials: P
authors.lastname: Bertone
mesh_terms: D000465:Algorithms; D000818:Animals; D017173:Caenorhabditis elegans; D019295:Computational Biology / Q000379:methods*; D004331:Drosophila melanogaster; D005091:Exons; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D007438:Introns; D022821:RNA Splice Sites; D012326:RNA Splicing; D012333:RNA, Messenger / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D022821:RNA Splice Sites; D012333:RNA, Messenger