相关实验视频

Updated: Jul 9, 2025

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Seq2science:功能基因组学分析的端到端工作流

Maarten van der Sande¹, Siebren Frölich¹, Tilman Schäfers¹

¹Molecular Developmental Biology, Radboud University Nijmegen, Nijmegen, the Netherlands.

|November 29, 2023

概括

Seq2science是一个多功能的工作流程,用于分析公共数据库中的功能基因组学数据. 它为多种物种的多种测序类型标准化了预处理,质量控制和分析.

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.

背景情况:

功能性基因组测序数据库为基因组规模分析提供了大量资源.
重新分析和整合公共数据与特定项目的数据集是有价值的,但由于标准化和可重复性问题而具有挑战性.
当前的基因组实验技术使得对众多物种的分析成为可能.

研究的目的:

介绍Seq2science,一个旨在简化功能基因组测序数据分析的多用途工作流.
为了方便从主要测序数据库和基因组组装源中检索数据.
为各种基因组实验提供标准化和可重复的分析管道.

主要方法:

Seq2science自动地从NCBI SRA,EBI ENA,DDBJ,GSA和ENCODE下载数据. 这是一个非常简单的程序.
它从Ensembl,NCBI和UCSC获取基因组组件.
工作流使用Snakemake语言与各种计算基础设施兼容,包括ATAC,RNA和ChIP-seq分析.

主要成果:

Seq2science涵盖了预处理,质量控制,可视化和分析步骤.
它支持通用和高级分析,如差异基因表达和动机分析.
该工作流已在多种物种上成功测试,证明了其多功能性.

结论:

Seq2science为功能基因组学数据分析提供了一个标准化和可重复的解决方案.
它简化了公共和项目特定数据的整合,加速了研究.
工作流程提高了大规模基因组数据集的可访问性和实用性.

关键词:

ATAC-seqq 的使用情况.在 ChIP-seqq.国家储备系统 (NGS)在RNA-seqqq.工作流的工作流.

更多相关视频

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Optimization for Sequencing and Analysis of Degraded FFPE-RNA Samples

Published on: June 8, 2020

相关概念视频

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.

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...