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通过TransBorrow算法进行转录组组合的协议

Dengyi Zhao¹, Juntao Liu¹, Ting Yu²

¹School of Mathematics and Statistics, Shandong University, Weihai 264209, China.

Biology methods & protocols

|November 29, 2023

概括

TransBorrow是一个新的软件,用于组装短RNA-seq读成全长的转录. 该工具通过提供快速准确的转录组装和表达量化来帮助转录组分析.

科学领域:

基因组学就是基因组学.
生物信息学是一种生物信息学.
分子生物学分子生物学

背景情况:

高通量RNA测序 (RNA-seq) 产生了大量用于转录组分析的数据.
来自RNA-seq的短读长为准确的全长转录组装带来了挑战.
有效的工具对于从短阅读中组装和量化转录表达至关重要.

研究的目的:

介绍TransBorrow,一个用于转录组装的新型软件工具.
为利用TransBorrow与短RNA-seq读取提供一个协议.
为了使短读数据的转录组能够进行快速,准确和灵活的分析.

主要方法:

开发了TransBorrow,这是一个针对短读量优化的转录组装软件.
集成的TransBorrow与拼接意识的对齐工具 (例如,Hisat2,Star).
结合TransBorrow与现有的转录组组装器 (例如,StringTie,袖口链,贝贝).
详细介绍了一个全面的协议,从原始数据处理到表达式量化.

主要成果:

通过TransBorrow,可以从简短的RNA-seq读取中组装全长的转录.
该协议可以准确量化表达的转录丰度.
该方法旨在在不同的计算平台上实现速度和灵活性.

结论:

TransBorrow提供了一种有效的解决方案,用于使用简短的RNA-seq读数进行转录组组.
该协议提供了一个完整的工作流程,用于分析短读RNA-seq数据.
这种方法提高了高通量测序对转录组学研究的实用性.

关键词:

在RNA-seq数据数据中.拼接的变种拼接的变种转录基因组组合组件

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Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

Protein Complex Assembly

Protein Complex Assembly

Transfer RNA Synthesis

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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...