Document type
ArticleVersion
Published versionPublication date
Publication license
Please use this identifier to cite or link to this item: https://hdl.handle.net/2445/208689
Assessment of transcript reconstruction methods for RNA-seq
Journal Title
Director/Tutor
Journal ISSN
Volume Title
Related resource
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.
Subject
Subject (English)
Citation
Citation
STEIJGER, Tamara, et al. Assessment of transcript reconstruction methods for RNA-seq. Nature Methods. 2013. Vol. 10, num. 12, pags. 1177-1184. ISSN 1548-7091. [consulted: 10 of August of 2026]. Available at: https://hdl.handle.net/2445/208689