Assessment of transcript reconstruction methods for RNA-seq.

Détails

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Etat: Public
Version: Final published version
Licence: CC BY-NC-SA 4.0
ID Serval
serval:BIB_63C268AABFEF
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Assessment of transcript reconstruction methods for RNA-seq.
Périodique
Nature Methods
Auteur⸱e⸱s
Steijger T., Abril J.F., Engström P.G., Kokocinski F., Abril J.F., Abril J.F., Akerman M., Alioto T., Ambrosini G., Antonarakis S.E., Behr J., Bertone P., Bohnert R., Bucher P., Cloonan N., Derrien T., Djebali S., Du J., Dudoit S., Engström P.G., Gerstein M., Gingeras T.R., Gonzalez D., Grimmond S.M., Guigó R., Habegger L., Harrow J., Hubbard T.J., Iseli C., Jean G., Kahles A., Kokocinski F., Lagarde J., Leng J., Lefebvre G., Lewis S., Mortazavi A., Niermann P., Rätsch G., Reymond A., Ribeca P., Richard H., Rougemont J., Rozowsky J., Sammeth M., Sboner A., Schulz M.H., Searle S.M., Solorzano N.D., Solovyev V., Stanke M., Steijger T., Stevenson B.J., Stockinger H., Valsesia A., Weese D., White S., Wold B.J., Wu J., Wu T.D., Zeller G., Zerbino D., Zhang M.Q., Hubbard T.J., Guigó R., Harrow J., Bertone P.
Collaborateur⸱rice⸱s
RGASP Consortium
ISSN
1548-7105 (Electronic)
ISSN-L
1548-7091
Statut éditorial
Publié
Date de publication
2013
Volume
10
Numéro
12
Pages
1177-1184
Langue
anglais
Résumé
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.
Mots-clé
Algorithms, Animals, Caenorhabditis elegans, Computational Biology/methods, Drosophila melanogaster, Exons, Gene Expression Profiling, Genome, Humans, Introns, RNA Splice Sites, RNA Splicing, RNA, Messenger/metabolism, Sequence Analysis, RNA/methods, Software
Pubmed
Web of science
Open Access
Oui
Création de la notice
06/02/2014 14:56
Dernière modification de la notice
15/01/2021 7:09
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