Methods to Study Splicing from High-Throughput RNA Sequencing Data

  • Gael P. Alamancos
  • Eneritz Agirre
  • Eduardo Eyras
Part of the Methods in Molecular Biology book series (MIMB, volume 1126)


The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be analyzed has turned this into a challenging task. In the last few years, a plethora of tools have been developed, allowing researchers to process RNA-Seq data to study the expression of isoforms and splicing events, and their relative changes under different conditions. We provide an overview of the methods available to study splicing from short RNA-Seq data, which could serve as an entry point for users who need to decide on a suitable tool for a specific analysis. We also attempt to propose a classification of the tools according to the operations they do, to facilitate the comparison and choice of methods.

Key words

RNA-Seq Splicing Alternative splicing Isoform Quantification Reconstruction 



We thank Y. Xing, K. Hertel, J.R. González, M. Kreitzman, and P. Drewe for comments and suggestions. This work was supported by the Spanish Ministry of Science with grants BIO2011-23920 and CSD2009-00080 and by Sandra Ibarra Foundation for Cancer with grant FSI 2011-035.


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Copyright information

© Springer Science+Business Media, LLC 2014

Authors and Affiliations

  • Gael P. Alamancos
    • 1
  • Eneritz Agirre
    • 1
  • Eduardo Eyras
    • 1
  1. 1.Computational GenomicsUniversitat Pompeu FabraBarcelonaSpain

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