Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Cole Trapnell, Brian A. Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J. Van Baren, Steven L Salzberg, Barbara J. Wold, Lior Pachter

Research output: Contribution to journalArticle

Abstract

High-throughput mRNA sequencing (RNA-Seq) promises simultaneous transcript discovery and abundance estimation. However, this would require algorithms that are not restricted by prior gene annotations and that account for alternative transcription and splicing. Here we introduce such algorithms in an open-source software program called Cufflinks. To test Cufflinks, we sequenced and analyzed

Original languageEnglish (US)
Pages (from-to)511-515
Number of pages5
JournalNature Biotechnology
Volume28
Issue number5
DOIs
StatePublished - May 2010
Externally publishedYes

Fingerprint

RNA
Cell Differentiation
Protein Isoforms
Molecular Sequence Annotation
High-Throughput Nucleotide Sequencing
Alternative Splicing
Transcription
Software
Genes
Throughput
Messenger RNA
Open source software

ASJC Scopus subject areas

  • Applied Microbiology and Biotechnology
  • Biotechnology
  • Molecular Medicine
  • Bioengineering
  • Biomedical Engineering

Cite this

Trapnell, C., Williams, B. A., Pertea, G., Mortazavi, A., Kwan, G., Van Baren, M. J., ... Pachter, L. (2010). Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28(5), 511-515. https://doi.org/10.1038/nbt.1621

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. / Trapnell, Cole; Williams, Brian A.; Pertea, Geo; Mortazavi, Ali; Kwan, Gordon; Van Baren, Marijke J.; Salzberg, Steven L; Wold, Barbara J.; Pachter, Lior.

In: Nature Biotechnology, Vol. 28, No. 5, 05.2010, p. 511-515.

Research output: Contribution to journalArticle

Trapnell, C, Williams, BA, Pertea, G, Mortazavi, A, Kwan, G, Van Baren, MJ, Salzberg, SL, Wold, BJ & Pachter, L 2010, 'Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation', Nature Biotechnology, vol. 28, no. 5, pp. 511-515. https://doi.org/10.1038/nbt.1621
Trapnell, Cole ; Williams, Brian A. ; Pertea, Geo ; Mortazavi, Ali ; Kwan, Gordon ; Van Baren, Marijke J. ; Salzberg, Steven L ; Wold, Barbara J. ; Pachter, Lior. / Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. In: Nature Biotechnology. 2010 ; Vol. 28, No. 5. pp. 511-515.
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