Methods to study splicing from high-throughput RNA sequencing data

Gael P. Alamancos, Eneritz Agirre, Eduardo Eyras

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review

51 Citations (Scopus)

Abstract

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.

Original languageEnglish
Title of host publicationSpliceosomal Pre-mRNA Splicing
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages357-397
Number of pages41
ISBN (Print)9781627039796
DOIs
Publication statusPublished - 2014
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1126
ISSN (Print)1064-3745

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