---
tags:
  - Free
catalog:
  name: MACS2/3
  description: ChIP-Seq analysis tool
  license_type: Free
  disciplines:
    - Biosciences
  available_on:
    - Puhti
---

# MACS2/3



MACS (Model-based Analysis of ChIP-Seq) is an analysis tool for NGS ChIP-Seq data.
MACS empirically models the length of the sequenced ChIP fragments and uses it to improve
the spatial resolution of predicted binding sites.

MACS also uses a dynamic Poisson distribution to effectively capture local biases in the
genome sequence, allowing for more sensitive and robust prediction. MACS compares can be
used for ChIP-Seq with or without control samples.

[TOC]

## License

Free to use and open source under [BSD 3-Clause License](https://raw.githubusercontent.com/macs3-project/MACS/master/LICENSE).

## Available



-  Puhti: 2.2.7.1, 3.0.0a7, 3.0.1
-  Chipster graphical user interface

## Usage

To check installed version on Puhti run command:

```bash
module spider macs
```

To set up MACS2 or MACS3 commands in puhti, give command:

```bash
module load macs/<version>
```

For example

After that you can start MACS with command:

```bash
module load macs/2.2.7.1
macs2 -h
```

or

```bash
module load macs/3.0.1
macs3 -h
```

Short MACS jobs can be executed as [interactive batch jobs](../computing/running/interactive-usage.md) in Puhti. Longer jobs should be run as [batch jobs](../computing/running/getting-started.md).


## More information

   *   [MACS2 in GitHub](https://github.com/taoliu/MACS/)
   *   [MACS3 in GitHub](https://github.com/macs3-project/MACS/)
