Deep Computational Circular RNA Analytics from RNA-seq Data
Deep Computational Circular RNA Analytics from RNA-seq Data
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DOI：
10.1007/978-1-4939-7562-4_2
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发表时间：
2018-01-01
期刊：
影响因子：
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通讯作者：
Dieterich, Christoph
中科院分区：
文献类型：
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作者：
Jakobi, Tobias;Dieterich, Christoph
环状RNA（circRNA）在20世纪90年代首次被描述为“乱序外显子”。CircRNA来源于线性RNA模板的反向剪接或外显子跳跃，近年来由于高通量全转录组测序方法的可用性而不断受到关注。许多手稿描述了在单细胞和多细胞真核生物物种中的数千种circRNA，并证明它们在特定组织或条件下是保守的，稳定的和丰富的。这份手稿提供了我们的生物信息学工具箱的一个演练，它涵盖了计算机模拟circRNA分析的各个方面，从原始测序数据和反向剪接接头发现到circRNA定量和内部circRNA结构的重建。
Circular RNAs (circRNAs) have been first described as "scrambled exons" in the 1990s. CircRNAs originate from back splicing or exon skipping of linear RNA templates and have continuously gained attention in recent years due to the availability of high-throughput whole-transcriptome sequencing methods. Numerous manuscripts describe thousands of circRNAs throughout uni- and multicellular eukaryote species and demonstrated that they are conserved, stable, and abundant in specific tissues or conditions. This manuscript provides a walk-through of our bioinformatics toolbox, which covers all aspects of in silico circRNA analysis, starting from raw sequencing data and back-splicing junction discovery to circRNA quantitation and reconstruction of internal the circRNA structure.