Related Experiment Video
Updated: May 24, 2026
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
Summary
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.
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.
Related Concept Videos
03:21RNA-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...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while microarray-based...
02:24Ribosome 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...
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...