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Related Concept Videos

RNA-seq03:21

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 microarray-based...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Related Experiment Video

Updated: May 24, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

RAGER: A user-friendly computational platform for integrated analysis of RNA-Seq and ATAC-seq data.

Yunjie Liu1, Yijia Liu2, Zhouming Zhang3

  • 1Jiangxi Provincial Key Laboratory of Tumor Biology, School of Basic Medicine, Jiangxi Medical College, Nanchang University, China.

Plos One
|May 22, 2026
PubMed
Summary
This summary is machine-generated.

RAGER is a new bioinformatics platform that integrates RNA sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) data. This tool simplifies the joint analysis of gene expression and chromatin accessibility, enabling faster biological discovery.

More Related Videos

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Related Experiment Videos

Last Updated: May 24, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes
05:07

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations
11:52

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • RNA sequencing (RNA-seq) and ATAC-seq are powerful genome-wide techniques for studying gene expression and regulation.
  • Interpreting complex RNA-seq and ATAC-seq datasets requires specialized bioinformatics expertise, posing a significant challenge.
  • Existing bioinformatics platforms often lack user-friendliness and integration capabilities for joint analysis.

Purpose of the Study:

  • To develop a user-friendly computational platform, RAGER, for the integrated analysis of RNA-seq and ATAC-seq data.
  • To automate the joint mining of transcriptome and chromatin accessibility data, reducing the need for extensive bioinformatics knowledge.
  • To accelerate biological discovery by simplifying and speeding up the processing of multi-omics sequencing data.

Main Methods:

  • RAGER integrates popular bioinformatics tools into an automated workflow using Snakemake.
  • The platform facilitates the joint analysis of RNA sequencing (RNA-seq) and Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) data.
  • The utility of RAGER was demonstrated by characterizing transcriptome and chromatin accessibility in two published datasets.

Main Results:

  • RAGER provides an automated workflow for the integrative analysis of RNA-seq and ATAC-seq data.
  • The platform significantly reduces processing time and the requirement for bioinformatics expertise.
  • RAGER successfully facilitated the characterization of gene expression and chromatin accessibility in tested datasets, supporting novel biological insights.

Conclusions:

  • RAGER is an effective computational platform for the joint analysis of RNA-seq and ATAC-seq data.
  • The automated workflow streamlines complex genomic analyses, making them more accessible to researchers.
  • RAGER has the potential to accelerate discoveries in gene regulation and molecular biology.