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Methods Mol Biol. 2012;883:97-110. doi: 10.1007/978-1-61779-839-9_7.

Detection and quantification of alternative splicing variants using RNA-seq.

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


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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