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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 11, 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

Computational analysis of bacterial RNA-Seq data.

Ryan McClure1, Divya Balasubramanian, Yan Sun

  • 1Department of Microbiology, Boston University School of Medicine, Boston, MA 02118, USA.

Nucleic Acids Research
|May 30, 2013
PubMed
Summary
This summary is machine-generated.

Rockhopper is a new open-source software for analyzing bacterial RNA sequencing (RNA-seq) data. It provides accurate transcriptome maps and aids in discovering novel bacterial genes and regulatory elements.

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Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

Related Experiment Videos

Last Updated: May 11, 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

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2
10:10

Three Differential Expression Analysis Methods for RNA Sequencing: limma, EdgeR, DESeq2

Published on: September 18, 2021

Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • High-throughput RNA sequencing (RNA-seq) has advanced bacterial transcriptome studies.
  • Existing computational methods struggle to keep pace with the volume of RNA-seq data.

Purpose of the Study:

  • To develop novel algorithms and an open-source software system (Rockhopper) for bacterial RNA-seq data analysis.
  • To improve the efficiency and accuracy of bacterial transcriptome analysis.

Main Methods:

  • Development of new algorithms tailored to bacterial gene structures.
  • Implementation of algorithms in the open-source Rockhopper software.
  • Testing Rockhopper using 2.1 billion reads from 75 RNA-seq experiments across five bacterial species.

Main Results:

  • Rockhopper accurately constructs bacterial transcriptome maps, validated against experimental data.
  • The system successfully identified novel small RNAs, operons, and transcription start sites.
  • Demonstrated high accuracy and efficiency in analyzing large-scale bacterial RNA-seq datasets.

Conclusions:

  • Rockhopper offers an efficient and accurate solution for bacterial RNA-seq data analysis.
  • The software facilitates the elucidation of bacterial transcriptomes, including gene expression and regulatory elements.