Alamancos Gael P, Agirre Eneritz, Eyras Eduardo
Computational Genomics, Universitat Pompeu Fabra, Barcelona, Spain.
Methods Mol Biol. 2014;1126:357-97. doi: 10.1007/978-1-62703-980-2_26.
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.
用于RNA的新型高通量测序（HTS）方法（RNA测序）的发展，为以前所未有的深度研究多种条件下的剪接提供了一种非常强大的手段。然而，待分析信息的复杂性已使其成为一项具有挑战性的任务。在过去几年中，已经开发出大量工具，使研究人员能够处理RNA测序数据，以研究异构体和剪接事件的表达，以及它们在不同条件下的相对变化。我们概述了可用于从短RNA测序数据研究剪接的方法，这可以作为需要为特定分析选择合适工具的用户的切入点。我们还尝试根据工具所执行的操作对其进行分类，以便于方法的比较和选择。
