Assessment of transcript reconstruction methods for RNA-seq.

Details

Serval ID
serval:BIB_63C268AABFEF
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Assessment of transcript reconstruction methods for RNA-seq.
Journal
Nature Methods
Author(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.
Working group(s)
RGASP Consortium
ISSN
1548-7105 (Electronic)
ISSN-L
1548-7091
Publication state
Published
Issued date
2013
Volume
10
Number
12
Pages
1177-1184
Language
english
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.
Keywords
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
Yes
Create date
06/02/2014 14:56
Last modification date
20/08/2019 14:20
Usage data