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Related Concept Videos

RNA-seq03:21

RNA-seq

11.6K
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...
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Ribosome Profiling02:24

Ribosome Profiling

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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...
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Related Experiment Video

Updated: Dec 26, 2025

3' End Sequencing Library Preparation with A-seq2
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RASflow: an RNA-Seq analysis workflow with Snakemake.

Xiaokang Zhang1, Inge Jonassen2

  • 1Computational Biology Unit, Department of Informatics, University of Bergen, Thormohlens Gate 55, Bergen, 5009, Norway.

BMC Bioinformatics
|March 19, 2020
PubMed
Summary
This summary is machine-generated.

Researchers can now easily analyze RNA sequencing (RNA-Seq) data with RASflow, a flexible workflow supporting diverse organisms and analysis types. This user-friendly tool simplifies gene expression studies for scientists of all skill levels.

Keywords:
RNA-SeqSnakemakeWorkflow

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Decreasing DNA sequencing costs drive increased RNA-Seq data generation, offering insights into gene expression and regulation.
  • RNA-Seq data requires processing for gene/transcript expression quantification, with existing workflows often limited in scope.
  • A need exists for a general, user-friendly RNA-Seq workflow applicable to diverse organisms and analysis approaches.

Purpose of the Study:

  • To develop a maximally general RNA-Seq analysis workflow.
  • To support research on both model and non-model organisms.
  • To create a workflow usable by individuals with limited programming skills.

Main Methods:

  • Developed the RNA-Seq Analysis Snakemake Workflow (RASflow) using Snakemake and Conda.
  • RASflow is modular, flexible, and user-friendly, addressing dependency and version conflicts.
  • Supports read mapping to both genomic and transcriptomic assemblies for broad applicability.

Main Results:

  • RASflow ensures reproducibility through Snakemake and Conda.
  • The workflow accommodates a wide range of applications and organisms.
  • RASflow requires no programming skills, making it accessible to researchers with diverse backgrounds.

Conclusions:

  • RASflow provides a simple and reliable RNA-Seq analysis solution.
  • The workflow is suitable for numerous research use cases.
  • RASflow enhances accessibility to RNA-Seq data analysis.