Salmon provides fast and bias-aware quantification of transcript expression View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2017-03-06

AUTHORS

Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford

ABSTRACT

Salmon is a computational tool that uses sample-specific models and a dual-phase inference procedure to correct biases in RNA-seq data and rapidly quantify transcript abundances.

PAGES

417-419

References to SciGraph publications

  • 2013-01-01. Streaming fragment assignment for real-time analysis of sequencing experiments in NATURE METHODS
  • 2016-09-26. Modeling of RNA-seq fragment sequence bias reduces systematic errors in transcript abundance estimation in NATURE BIOTECHNOLOGY
  • 2011-02-10. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads in GENOME BIOLOGY
  • 2014-04-20. Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms in NATURE BIOTECHNOLOGY
  • 2014-08-24. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium in NATURE BIOTECHNOLOGY
  • 2013-09-15. Transcriptome and genome sequencing uncovers functional variation in humans in NATURE
  • 2011-04-19. Estimation of alternative splicing isoform frequencies from RNA-Seq data in ALGORITHMS FOR MOLECULAR BIOLOGY
  • 2011-03-16. Improving RNA-Seq expression estimates by correcting for fragment bias in GENOME BIOLOGY
  • 2016-04-23. A benchmark for RNA-seq quantification pipelines in GENOME BIOLOGY
  • 2013-11-01. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories in NATURE BIOTECHNOLOGY
  • 2014-12-12. TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads in BMC GENOMICS
  • 2013-09-26. The Cancer Genome Atlas Pan-Cancer analysis project in NATURE GENETICS
  • 2016-04-04. Near-optimal probabilistic RNA-seq quantification in NATURE BIOTECHNOLOGY
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1038/nmeth.4197

    DOI

    http://dx.doi.org/10.1038/nmeth.4197

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1084129290

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/28263959


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