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

Interpreting Run Charts01:25

Interpreting Run Charts

2.7K
Run charts, essentially line graphs plotted over time, serve as fundamental yet effective tools for process analysis. They chronicle data sequentially, facilitating the identification of trends, shifts, or cyclical movements. This graphical representation is instrumental in determining whether a process is stable or exhibits signs of potential instability indicative of special cause variation. In the healthcare domain, run charts depict infection rates over time, enabling hospitals to monitor...
2.7K
Wald-Wolfowitz Runs Test I01:17

Wald-Wolfowitz Runs Test I

746
The Wald-Wolfowitz test, also known as the runs test, is a nonparametric statistical test used to assess the randomness of a sequence of two different types of elements (e.g., positive/negative values, successes/failures). It examines whether the order of the elements in a sequence is random or if there is a pattern or trend present. This nonparametric test applies to any ordered data despite the population and sample data distribution, even if a higher sample size is available.
The test works...
746
Run Charts01:12

Run Charts

114
Run charts serve as an essential instrument for visualizing the performance of various processes over time, enabling the identification of trends and patterns crucial for quality improvement. These charts map out a series of data points chronologically, offering insights into the stability and efficiency of a process. A run chart's creation involves plotting data points on a graph, with the time intervals on the horizontal axis and the specific measurements on the vertical axis. For...
114
Multiple Comparison Tests01:13

Multiple Comparison Tests

4.0K
Multiple comparison test, abbreviated as MCT, is a post hoc analysis generally performed after comparing multiple samples with one or more tests. An MCT will help identify a significantly different sample among multiple samples or a factor among multiple factors.
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...
4.0K
Kaplan-Meier Approach01:24

Kaplan-Meier Approach

277
The Kaplan-Meier estimator is a non-parametric method used to estimate the survival function from time-to-event data. In medical research, it is frequently employed to measure the proportion of patients surviving for a certain period after treatment. This estimator is fundamental in analyzing time-to-event data, making it indispensable in clinical trials, epidemiological studies, and reliability engineering. By estimating survival probabilities, researchers can evaluate treatment effectiveness,...
277
Production Efficiency01:01

Production Efficiency

17.1K
Net production efficiency (NPE) is the efficiency at which organisms assimilate energy into biomass for the next trophic level. Due to low metabolic rates and less energy spent on thermoregulatory processes, the NPE of ectotherms (cold-blooded animals) is 10 times higher than endotherms (warm-blooded animals).
17.1K

You might also read

Related Articles

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

Sort by
Same author

Chromatin accessibility landscapes define stromal cell identities across tissues.

Communications biology·2026
Same author

Adaptive introgression in modern human circadian rhythm genes.

Npj biological timing and sleep·2025
Same author

Archaic adaptive introgression in modern human reproductive genes.

Communications biology·2025
Same author

Mapping the 3D genome architecture.

Computational and structural biotechnology journal·2025
Same author

Chimeric Antigen Receptor-T Cells in Colorectal Cancer: Pioneering New Avenues in Solid Tumor Immunotherapy.

Journal of clinical oncology : official journal of the American Society of Clinical Oncology·2025
Same author

Global and local ancestry estimation in a captive baboon colony.

PloS one·2024

Related Experiment Video

Updated: Sep 18, 2025

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

2.9K

Benchmarking peak calling methods for CUT&RUN.

Amin Nooranikhojasteh1, Ghazaleh Tavallaee1, Elias Orouji1

  • 1Princess Margaret Cancer Centre, University Health Network (UHN), Toronto, ON M5G 1L7, Canada.

Bioinformatics (Oxford, England)
|June 26, 2025
PubMed
Summary

Benchmarking Cleavage Under Targets and Release Using Nuclease (CUT&RUN) peak callers revealed significant performance variations. Selecting the optimal tool is crucial for accurate protein-DNA interaction mapping and understanding chromatin dynamics.

More Related Videos

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
07:35

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

795
Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells
10:10

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

2.6K

Related Experiment Videos

Last Updated: Sep 18, 2025

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

2.9K
Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data
07:35

Author Spotlight: A Computational Pipeline for Analyzing Chimeric Noncoding RNA-Target RNA Interactions in High-Throughput Sequencing Data

Published on: December 1, 2023

795
Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells
10:10

Author Spotlight: Cistrome Analysis in Mouse Muscle Stem Cells

Published on: July 7, 2023

2.6K

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is a powerful technique for mapping protein-DNA interactions, particularly histone modifications.
  • Accurate peak identification is essential for the success of CUT&RUN experiments, but optimal peak calling methods for its data are not well-established.

Purpose of the Study:

  • To benchmark the performance of four prominent peak calling tools (MACS2, SEACR, GoPeaks, LanceOtron) for CUT&RUN data.
  • To evaluate these tools based on peak number, length distribution, signal enrichment, and reproducibility.
  • To guide the selection of appropriate peak callers for CUT&RUN experiments.

Main Methods:

  • Benchmarking of MACS2, SEACR, GoPeaks, and LanceOtron using CUT&RUN datasets.
  • Analysis of three histone marks (H3K4me3, H3K27ac, H3K27me3) in mouse brain tissue.
  • Inclusion of data from the 4D Nucleome database for comprehensive evaluation.

Main Results:

  • Significant variability was observed in the peak calling performance of the evaluated tools.
  • Each peak caller exhibited distinct strengths and weaknesses concerning sensitivity, precision, and applicability to different histone marks.
  • Performance varied based on the specific histone mark analyzed, highlighting the need for tailored approaches.

Conclusions:

  • The choice of peak calling tool significantly impacts the identification of regions of interest in CUT&RUN experiments.
  • Understanding the performance characteristics of different callers is essential for high-confidence data analysis.
  • This study provides critical insights for selecting optimal peak callers to advance the study of chromatin dynamics and transcriptional regulation.