Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Type 2 diabetes prevention programs at the community and municipal level: a scoping review of controlled intervention studies.

BMC public health·2026

Same author

Clinical decision support in hematological malignancies using a case-grounded AI agent.

Nature medicine·2026

Same author

Quick assessment of quality-of-life in itch: An exploratory validation of the 5-item pruritus life quality.

Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG·2026

Same author

High-Frequency Global Postoperative Status PROMs Track Pain Peaks and Analgesic Use After Degenerative Lumbar Spine Surgery.

Global spine journal·2026

Same author

Early pain relief and segmental realignment after two-stage lateral lumbar interbody fusion (LLIF) with posterior instrumentation in degenerative lumbar pathology.

Neurosurgical review·2026

Same author

LLM4ODM: Synthetic Clinical Study Data Generation for CDISC ODM.

Studies in health technology and informatics·2026

Same journal

3DICE: Interpretable 3D Cross-Modal Learning for Drug-Target Interaction Prediction and Large-Scale Drug Discovery.

Bioinformatics (Oxford, England)·2026

Same journal

KASSPer: Kinase Active Site Structure Prediction using Protein and Ligand Language Models and Its Application to Virtual Screening.

Bioinformatics (Oxford, England)·2026

Same journal

IDR searcher: a search engine solution for public image resources.

Bioinformatics (Oxford, England)·2026

Same journal

KCFtools: Rapid alignment-free method for introgression screening and GWAS using k-mer profiles.

Bioinformatics (Oxford, England)·2026

Same journal

Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.

Bioinformatics (Oxford, England)·2026

Same journal

conMItion: an R package adjusting confounding factors for associations in multi-omics.

Bioinformatics (Oxford, England)·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Apr 26, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data.

Carolin Walter¹, Daniel Schuetzmann¹, Frank Rosenbauer¹

¹Institute of Medical Informatics, University of Münster, 48149 Münster, Germany, and Institute of Molecular Tumorbiology, University of Münster, 48149 Münster, Germany.

Bioinformatics (Oxford, England)

|August 1, 2014

Summary

This summary is machine-generated.

Basic4Cseq is a new R/Bioconductor package for analyzing 4C-seq data, offering filtering, quality control, and visualization of genomic interactions. It simplifies the processing of 4C-seq (Circular Chromosome Conformation Capture sequencing) data from raw reads to insightful visualizations.

More Related Videos

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

Related Experiment Videos

Last Updated: Apr 26, 2026

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

4C-seq (Circular Chromosome Conformation Capture sequencing) is a powerful technique for studying genome-wide interactions.
Analyzing 4C-seq data involves complex steps from raw reads to interpretable results.
Existing tools may lack comprehensive functionalities for basic filtering, analysis, and visualization.

Purpose of the Study:

To introduce Basic4Cseq, an R/Bioconductor package designed for the comprehensive analysis of 4C-seq data.
To provide users with essential tools for filtering, quality control, and visualization of 4C-seq experimental results.
To facilitate the near-cis visualization of genomic interactions derived from 4C-seq experiments.

Main Methods:

The package processes aligned 4C-seq raw data in Binary Alignment/Map (BAM) format.
It maps short reads to a virtual fragment library, including functions to create these libraries.
Includes optional filters for invalid reads and 4C-seq fragments, alongside basic quality controls.

Main Results:

Basic4Cseq enables the creation of virtual fragment libraries with detailed genomic information.
The package offers filtering capabilities for BAM files and 4C-seq fragments to refine data quality.
Visualizations include coverage plots and multi-scale contact profiles for data in the vicinity of the viewpoint.

Conclusions:

Basic4Cseq provides a user-friendly and efficient R/Bioconductor package for 4C-seq data analysis.
The package supports the entire workflow from raw data processing to advanced visualization.
Export options for Wig and CSV files allow for further analysis and integration with other bioinformatics tools.