Manananggal - a novel viewer for alternative splicing events.
Manananggal - a novel viewer for alternative splicing events.
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DOI：
10.1186/s12859-017-1548-5
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发表时间：
2017-02-21
影响因子：
3
通讯作者：
Birzele F
中科院分区：
文献类型：
--
作者：
Barann M;Zimmer R;Birzele F
选择性剪接是一种重要的细胞机制，可以通过RNA测序进行分析。然而，以自动方式识别剪接事件容易出错。因此，需要进一步验证以选择可替代剪接事件(AS)的可靠实例。只有几个工具专门设计用于交互检查AS，而且现有的可视化方法可以得到显着改进。在这里，我们介绍Mananangga，一个专门为识别下一代测序数据中的剪接事件而设计的应用程序。Mananangga包括一个用于视觉检查的Web应用程序和一个允许ASE检测的命令行工具。我们将IGV查看器、DEXSeq拼接图和SpliceSeq中的生鱼片图与Mananangal界面进行了比较，并讨论了这些工具的优缺点。我们表明，生鱼片(如IGV查看器和SpliceSeq所使用的那些)为简单的ASE提供了一个实用的解决方案，但也指出了高度复杂基因的缺陷。Mananangga是一个交互式Web应用程序，提供了专门为识别其他工具所缺乏的可选剪接事件而量身定做的功能。选择亚型子集的能力允许更容易地解释复杂的选择性剪接事件。与SpliceSeq和DEXSeq剪接图不同，Mananangga没有通过显示完整的转录模型来掩盖基因结构，这使得更容易确定哪些异构体表达，哪些没有表达。本文的在线版本(doi：10.1186/s12859-0171548-5)包含补充材料，授权用户可以使用。
Alternative splicing is an important cellular mechanism that can be analyzed by RNA sequencing. However, identification of splicing events in an automated fashion is error-prone. Thus, further validation is required to select reliable instances of alternative splicing events (ASEs). There are only few tools specifically designed for interactive inspection of ASEs and available visualization approaches can be significantly improved. Here, we present Manananggal, an application specifically designed for the identification of splicing events in next generation sequencing data. Manananggal includes a web application for visual inspection and a command line tool that allows for ASE detection. We compare the sashimi plots available in the IGV Viewer, the DEXSeq splicing plots and SpliceSeq to the Manananggal interface and discuss the advantages and drawbacks of these tools. We show that sashimi plots (such as those used by the IGV Viewer and SpliceSeq) offer a practical solution for simple ASEs, but also indicate short-comings for highly complex genes. Manananggal is an interactive web application that offers functions specifically tailored to the identification of alternative splicing events that other tools are lacking. The ability to select a subset of isoforms allows an easier interpretation of complex alternative splicing events. In contrast to SpliceSeq and the DEXSeq splicing plot, Manananggal does not obscure the gene structure by showing full transcript models that makes it easier to determine which isoforms are expressed and which are not. The online version of this article (doi:10.1186/s12859-017-1548-5) contains supplementary material, which is available to authorized users.