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Detection and Quantification of Alternative Splicing Variants Using RNA-seq

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RNA Abundance Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 883))

Abstract

Next-generation sequencing has enabled genome-wide studies of alternative pre-mRNA splicing, allowing for empirical determination, characterization, and quantification of the expressed RNAs in a sample in toto. As a result, RNA sequencing (RNA-seq) has shown tremendous power to drive biological discoveries. At the same time, RNA-seq has created novel challenges that necessitate the development of increasingly sophisticated computational approaches and bioinformatic tools. In addition to the analysis of massive datasets, these tools also need to facilitate questions and analytical approaches driven by such rich data. HTS and RNA-seq are still in a stage of very rapid evolution and are, therefore, only introduced in general terms. This chapter mainly focuses on the methods for discovery, detection, and quantification of alternatively spliced transcript variants.

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Author information

Authors and Affiliations

  1. The Donald Danforth Plant Science Center, St. Louis, MO, USA

    Douglas W. Bryant Jr, Henry D. Priest & Todd C. Mockler

  2. Intuitive Genomics, Inc., St. Louis, MO, USA

    Douglas W. Bryant Jr

  3. Division of Biology and Biomedical Sciences, Washington University, St. Louis, MO, USA

    Henry D. Priest & Todd C. Mockler

Authors
  1. Douglas W. Bryant Jr
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  2. Henry D. Priest
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  3. Todd C. Mockler
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Corresponding author

Correspondence to Todd C. Mockler .

Editor information

Editors and Affiliations

  1. , Dept. Plant Pathology & Microbiology, University of California, University Avenue 900, Riverside, 92521, USA

    Hailing Jin

  2. , Division of Plant Sciences, University of Missouri, Agriculture Building 1-31, Columbia, 65211, Missouri, USA

    Walter Gassmann

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Bryant, D.W., Priest, H.D., Mockler, T.C. (2012). Detection and Quantification of Alternative Splicing Variants Using RNA-seq. In: Jin, H., Gassmann, W. (eds) RNA Abundance Analysis. Methods in Molecular Biology, vol 883. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-839-9_7

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  • DOI: https://doi.org/10.1007/978-1-61779-839-9_7

  • Published:

  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-838-2

  • Online ISBN: 978-1-61779-839-9

  • eBook Packages: Springer Protocols

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