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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: Jul 8, 2026

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

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis.

Syed Hussain Ather1, Olaitan Igbagbo Awe2, Thomas J Butler3

  • 1National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.

F1000Research
|October 6, 2020
PubMed
Summary
This summary is machine-generated.

SeqAcademy is a user-friendly markdown pipeline for analyzing RNA sequencing (RNA-Seq) and ChIP sequencing (ChIP-Seq) data. This tutorial introduces novice bioinformaticians to essential tools for biological insight from sequencing reads.

Keywords:
ChIP-SeqRNA-Seqalignmentdifferential gene expressioneducationpeak-callingpipelinetutorial

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Gene expression quantification and transcript structure characterization are key molecular biology challenges.
  • RNA sequencing (RNA-Seq) and ChIP sequencing (ChIP-Seq) are powerful but complex methods for beginners.
  • Existing pipelines often cater to advanced users, leaving a gap for novices.

Purpose of the Study:

  • To present SeqAcademy, a comprehensive tutorial for analyzing RNA-Seq and ChIP-Seq data.
  • To provide a user-friendly, start-to-finish pipeline for novice bioinformaticians.
  • To facilitate the analysis of public RNA-Seq and ChIP-Seq data.

Main Methods:

  • Developed a pipeline entirely in markdown language.
  • Integrated popular bioinformatics tools for RNA-Seq and ChIP-Seq analysis.
  • Utilized publicly available sequencing data and a yeast experiment for demonstration.

Main Results:

  • SeqAcademy offers a step-by-step guide from raw reads to biological insights.
  • The pipeline emphasizes practical and conceptual aspects of data analysis.
  • It bridges the gap between complex tools and novice users.

Conclusions:

  • SeqAcademy effectively introduces state-of-the-art RNA-Seq and ChIP-Seq analysis tools.
  • This resource empowers beginning bioinformaticians to analyze large public datasets.
  • It facilitates broader accessibility to genomic data analysis.