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相关概念视频

RNA-seq03:21

RNA-seq

10.0K
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...
10.0K
Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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相关实验视频

Updated: Jul 13, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

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TAGADA:一个可扩展的管道,以改善基因组注释与RNA-seq数据.

Cyril Kurylo1, Cervin Guyomar1, Sylvain Foissac1

  • 1GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, Toulouse, France.

NAR genomics and bioinformatics
|October 18, 2023
PubMed
概括

TAGADA是一个新的RNA-seq管道,通过组装,解构和分析转录和基因来改善基因组注释. 这种生物信息学工具可以增强基因模型,计算表达值,并识别长非编码RNA (lncRNAs).

科学领域:

  • 生物信息学是一种生物信息学.
  • 基因组学就是基因组学.
  • 文字转录学 (Transcriptomics) 是一个学科.

背景情况:

  • 基因组注释对于编目特定物种的基因和转录至关重要.
  • 将新的转录组数据集成到现有的注释中是必不可少的,但对于当前的生物信息学管道来说具有挑战性.
  • 现有的管道在利用新的RNA-sequencing (RNA-seq) 数据有效和一致地更新注释方面扎.

研究的目的:

  • 介绍TAGADA,一种新的RNA测序 (RNA-seq) 管道,旨在用于转录和基因组装,解卷和分析.
  • 用RNA-seq数据增强现有的基因模型并生成改进的基因组注释.
  • 为表达式值计算,长非编码RNA (lncRNA) 识别和质量控制提供全面的工具.

主要方法:

  • TAGADA处理基因组序列,参考注释,并读取RNA-seq.
  • 该管道使用Nextflow DSL2以实现用户友好的功能和容器化以实现可重复性.
  • 它将短读数 (Illumina NovaSeq) 与长读数 (PacBio Iso-Seq) 集成在一起,用于多功能分析.

主要成果:

  • 在和猪基因组中,TAGADA显著增加了注释转录的数量,约为[FORMULA].

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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
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Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

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相关实验视频

Last Updated: Jul 13, 2025

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples
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Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

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  • 管道成功计算了参考和新注释的表达式值.
  • TAGADA识别了长非编码转录 (lncRNAs),并提供了详细的质量控制报告.

    • 结论:

    • TAGADA提供了一种有效和可重复的解决方案,用于使用RNA-seq数据更新和改进基因组注释.
    • 管道集成多种读取类型 (短和长) 的能力提高了它的多功能性.
    • 通过提高基因模型的全面性,TAGADA显著推进了比较基因组学和转录基因组学领域.