StringTie enables improved reconstruction of a transcriptome from RNA-seq reads View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2015-02-18

AUTHORS

Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg

ABSTRACT

Using a network flow algorithm from optimization theory enables improved assembly of transcriptomes from RNA-seq reads.

PAGES

290-295

References to SciGraph publications

  • 2013-01-01. Streaming fragment assignment for real-time analysis of sequencing experiments in NATURE METHODS
  • 2010-05-02. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation in NATURE BIOTECHNOLOGY
  • 2011-08-04. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome in BMC BIOINFORMATICS
  • 2011-05-15. Full-length transcriptome assembly from RNA-Seq data without a reference genome in NATURE BIOTECHNOLOGY
  • 2013-04-25. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions in GENOME BIOLOGY
  • 2008-11-27. Alternative isoform regulation in human tissue transcriptomes in NATURE
  • 2011-05-27. Computational methods for transcriptome annotation and quantification using RNA-seq in NATURE METHODS
  • 2013-04-10. A novel min-cost flow method for estimating transcript expression with RNA-Seq in BMC BIOINFORMATICS
  • 2013-11-03. Assessment of transcript reconstruction methods for RNA-seq in NATURE METHODS
  • 2010-05-02. Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs in NATURE BIOTECHNOLOGY
  • 2011-12-14. Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study in BMC BIOINFORMATICS
  • <error retrieving object. in <ERROR RETRIEVING OBJECT
  • 2013-12-24. Blind spots of quantitative RNA-seq: the limits for assessing abundance, differential expression, and isoform switching in BMC BIOINFORMATICS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nbt.3122

    DOI

    http://dx.doi.org/10.1038/nbt.3122

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1045760294

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/25690850


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