Main logo
?
tutorial arrow
×
Create your own tool library
Bookmark tools and put favorites into folders to find them easily.

Model-based Analysis for ChIP-Seq MACS

A software to analyze data generated by short read sequencers. MACS empirically models the shift size of ChIP-Seq tags, and uses it to improve the spatial resolution of predicted binding sites. It offers four important utilities for predicting protein-DNA interaction sites from ChIP-Seq. First, it improves the spatial resolution of the predicted sites by empirically modeling the distance d and shifting tags by d/2. Second, MACS uses a dynamic λ local parameter to capture local biases in the genome and improves the robustness and specificity of the prediction. Third, MACS can be applied to ChIP-Seq experiments without controls, and to those with controls with improved performance. Last but not least, MACS is easy to use and provides detailed information for each peak.

User report

tutorial arrow
×
Vote up tools and offer feedback
Give value to tools and make your expertise visible
Give your feedback on this tool
Sign up for free to join and share with the community
Sort by:

1 user review

1 user review

Fabien Pichon's avatar image Fabien Pichon's country flag

Fabien Pichon

A very good software to find peaks in ChIP-seq experiments (except for broad peaks like H3K27me3 and H3K36me3 where you should prefer SICER). Also works perfectly with ATAC-seq where you can use it without input (-c option).
Easy to install and use.

MACS forum

tutorial arrow
×
Communicate with other users
Participate in the forum to get support for using tools. Ask questions about technical specifications.
Take part in the discussion
Sign up for free to ask question and share your advices

MACS classification

MACS specifications

Software type:
Package/Module
Restrictions to use:
None
Input format:
TXT, ELAND, BED, ELANDMULTI, ELANDEXPORT, ELANDMULTIPET, SAM, BAM, BOWTIE
Output format:
XLS, BED, R, WIG.GZ
Programming languages:
Python
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Input data:
A tag file, a treatment file
Output data:
Peaks, peak locations, negative peaks, model image, diagnosis report
Operating system:
Unix/Linux
License:
Artistic License version 2.0
Version:
1.4.2
Maintained:
Yes

MACS distribution

versioning

tutorial arrow
×
Upload and version your source code
Get a DOI for each update to improve tool traceability. Archive your releases so the community can easily visualize progress on your work.
Facilitate your tool traceability
Sign up for free to upload your code and get a DOI

No versioning.

download

MACS support

Documentation

Maintainer

  • Wei Li <>

Credits

tutorial arrow
×
Promote your skills
Define all the tasks you managed and assign your profile the appropriate badges. Become an active member.
Promote your work
Sign up for free to badge your contributorship

Publications

Institution(s)

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, MA, USA; Division of Molecular and Cellular Oncology, Department of Medical Oncology, Dana-Farber Cancer Institute and Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Gene Security Network, Inc., Redwood City, CA, USA; Molecular Pathology Unit and Center for Cancer Research, Massachusetts General Hospital and Department of Pathology, Harvard Medical School, Charlestown, MA, USA; Broad Institute of Harvard and MIT, Cambridge, MA, USA; Department of Genetics, Stanford University Medical Center, Stanford, CA, USA; Division of Biostatistics, Dan L Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA

Funding source(s)

NIH grants HG004069, HG004270 and DK074967

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.