Identification of novel transcripts in annotated genomes using RNA-Seq. Roberts, A., Pimentel, H., Trapnell, C., & Pachter, L. Bioinformatics (Oxford, England), 27(17):2325--9, September, 2011. ![Identification of novel transcripts in annotated genomes using RNA-Seq. [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex SUMMARY: We describe a new 'reference annotation based transcript assembly' problem for RNA-Seq data that involves assembling novel transcripts in the context of an existing annotation. This problem arises in the analysis of expression in model organisms, where it is desirable to leverage existing annotations for discovering novel transcripts. We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation. AVAILABILITY: The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http://bio.math.berkeley.edu/cufflinks. The software is released under the BOOST license. CONTACT: cole@broadinstitute.org; lpachter@math.berkeley.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
@article{roberts_identification_2011,
title = {Identification of novel transcripts in annotated genomes using {RNA}-{Seq}.},
volume = {27},
issn = {1367-4811},
url = {http://bioinformatics.oxfordjournals.org/content/27/17/2325},
doi = {10.1093/bioinformatics/btr355},
abstract = {SUMMARY: We describe a new 'reference annotation based transcript assembly' problem for RNA-Seq data that involves assembling novel transcripts in the context of an existing annotation. This problem arises in the analysis of expression in model organisms, where it is desirable to leverage existing annotations for discovering novel transcripts. We present an algorithm for reference annotation-based transcript assembly and show how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation. AVAILABILITY: The methods described in this article are implemented in the Cufflinks suite of software for RNA-Seq, freely available from http://bio.math.berkeley.edu/cufflinks. The software is released under the BOOST license. CONTACT: cole@broadinstitute.org; lpachter@math.berkeley.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
number = {17},
journal = {Bioinformatics (Oxford, England)},
author = {Roberts, Adam and Pimentel, Harold and Trapnell, Cole and Pachter, Lior},
month = sep,
year = {2011},
pmid = {21697122},
keywords = {Algorithms, Animals, Gene Expression Profiling, Genome, Humans, Messenger, Messenger: chemistry, Messenger: metabolism, Molecular Sequence Annotation, RNA, Sequence Analysis, Software},
pages = {2325--9}
}
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