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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...

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Updated: Jul 29, 2025

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

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

Published on: September 18, 2021

NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods.

Chantal Scheepbouwer^1,2,3, Michael Hackenberg^4,5,6,7, Monique A J van Eijndhoven^3,8

¹Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center (UMC) location Vrije Universiteit Amsterdam, Amsterdam 1081HV, The Netherlands.

Nucleic Acids Research

|May 22, 2023

Summary

This summary is machine-generated.

Technical artifacts in RNA sequencing can skew results. NormSeq is a new web tool that helps researchers select the best data normalization methods to ensure accurate biological insights from gene expression data.

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Last Updated: Jul 29, 2025

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Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Targeted RNA Sequencing Assay to Characterize Gene Expression and Genomic Alterations

Published on: August 4, 2016

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

RNA sequencing (RNA-seq) is a powerful tool for analyzing gene expression.
Technical variations during library preparation and data analysis can introduce artifacts.
Accurate data normalization is crucial for reliable RNA-seq analysis, especially with large or low-input datasets.

Purpose of the Study:

To develop a user-friendly web tool, NormSeq, for assessing RNA-sequencing data normalization methods.
To provide a systematic approach for selecting optimal normalization strategies to minimize non-biological variability.

Main Methods:

Development of NormSeq, a free web-server tool.
Implementation of information gain as a metric to evaluate normalization method performance.
Systematic assessment of various normalization techniques on given datasets.

Main Results:

NormSeq enables researchers to evaluate and compare different normalization methods.
The tool utilizes information gain to identify normalization strategies that best reduce technical noise.
Facilitates improved data quality and biological inference from RNA-seq experiments.

Conclusions:

NormSeq offers a valuable resource for researchers to optimize RNA-sequencing data normalization.
The tool empowers users, including those without extensive bioinformatics expertise, to achieve reliable biological interpretations.
Effective normalization is key to maximizing the utility of high-throughput RNA sequencing data.