Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

87.9K
The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
87.9K
Genomics02:02

Genomics

35.5K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.5K
Sanger Sequencing01:57

Sanger Sequencing

800.8K
DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
800.8K
Synthetic Biology02:55

Synthetic Biology

4.4K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
4.4K
DNA Microarrays02:34

DNA Microarrays

16.8K
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
16.8K
RNA-seq03:21

RNA-seq

9.4K
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...
9.4K

You might also read

Related Articles

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

Sort by
Same author

Mast cell homeostasis depends on KIT ligand from dermal fibroblasts and perivascular cells in mouse skin.

The Journal of investigative dermatology·2026
Same author

Lack of MDA5 delays hematopoietic aging by modulating inflammaging and proteostasis in mice.

Nature communications·2026
Same author

Complete chloroplast genome of the federally endangered Menzies' wallflower <i>Erysimum menziesii</i> (Brassicaceae, Anthophyta) from California, USA.

Microbiology resource announcements·2026
Same author

Common and rare variant analyses reveal genetic factors underlying idiopathic pulmonary fibrosis and its shared aetiology with severe COVID-19.

EBioMedicine·2025
Same author

Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis.

BMC research notes·2025
Same author

Lysosome-dependent nutrient scavenging underlies stress adaptation during epithelial-to-mesenchymal transition.

bioRxiv : the preprint server for biology·2025
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: Apr 30, 2026

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

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

Published on: December 13, 2024

3.7K

deepTools: a flexible platform for exploring deep-sequencing data.

Fidel Ramírez1, Friederike Dündar2, Sarah Diehl1

  • 1Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.

Nucleic Acids Research
|May 7, 2014
PubMed
Summary
This summary is machine-generated.

We developed deepTools, a user-friendly web server for analyzing deep sequencing data. This platform simplifies the visualization and processing of complex genomic data for researchers without extensive bioinformatics expertise.

More Related Videos

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

6.7K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.9K

Related Experiment Videos

Last Updated: Apr 30, 2026

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

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

Published on: December 13, 2024

3.7K
Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
09:14

Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens

Published on: June 28, 2018

6.7K
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms
10:41

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

9.9K

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Deep sequencing generates vast amounts of complex data.
  • Analyzing this data requires specialized bioinformatics skills.
  • Existing tools may lack standardization or user-friendliness.

Purpose of the Study:

  • To provide a standardized web server for processing and visualizing deep sequencing data.
  • To offer accessible tools for researchers with limited bioinformatics background.
  • To enable efficient and reproducible analysis of sequencing experiments.

Main Methods:

  • Development of a Galaxy-based web server.
  • Implementation of a suite of tools named deepTools.
  • Support for standard data formats and generation of heatmaps and summary plots.
  • Inclusion of tools for analyzing aligned reads and generating normalized coverage files.

Main Results:

  • deepTools provides a standardized platform for deep sequencing data analysis.
  • Users can easily upload data and generate customizable visualizations like heatmaps.
  • Efficient and reproducible generation of normalized coverage files is enabled.
  • The platform is modular, open-source, and expandable.

Conclusions:

  • deepTools lowers the barrier for deep sequencing data analysis.
  • It empowers researchers to explore their sequencing results effectively.
  • The web server facilitates standardized and reproducible genomic data exploration.