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Arpeggio provides you with a Java-based application designed to help researches compare multiple ChIP-seq datasets.
By comparing new genome data with annotated datasets, researchers can identify similar genomic patterns. Arpeggio can process many types of DNA-binding proteins and determine their biological properties.









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Arpeggio aims at providing a ‘one stop shopping’ solution for researchers to compare their results against the current public data without wasting time on the plethora of databases in use today.
Arpeggio integrates ChIP-seq peaks found by the Rpeak algorithm (version 1.1.1) along with several different types of ChIP-seq annotated tracks (gene transcription, histone modifications, PolII & PolIII) and inputs from the current genome assembly build. It provides a visual comparison based on customizable analysis parameters such as genomic coverage and similarity.
Arpeggio is separated into two functional modules:
A comparison module that can be used to compare the full genome (diploid or haploid) available in the RefSeq release.
A peak module that takes the user-selected genomic interval and provides the list of peaks as well as the genomic annotation for the selected interval.

Arpeggio is easy to use and can be installed in a reasonable time. The graphical user interface of Arpeggio is written using the Java Swing framework and offers users a simple easy to use interface with a variety of options in the comparison module. The main module is based on the pajek algorithm that is widely used for network visualization.

To make use of Arpeggio it is required to have the following data files in proper format:
A ChIP-seq track file (FASTA format) with a unique name for each sample
An experiment-related data file, normally a bed format (depending on the input format, it may have to be converted to bed or BED) file such as one produced by a peak caller.

Data file format

ChIP-seq track files must be in FASTA format to be processed by Arpeggio. It contains:
A unique suffix with the name of the experiment
A unique suffix for each sample
A suffix to the sequenced sample, for example:


where A is the sample name, 1, 2 and 3 are samples indexes.

Peak files must be in bed format, a basic format already used by the bedtools program. The bed format is a text file, delimited by “\t” (tabs). Each line should contain an aligned sequence with a unique identifier corresponding to the sample name. For example:
5 5100

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Arpeggio was downloaded from GitHub:

To install on a single Mac, see the instructions in the README file.
To install on a Mac cluster, see instructions here.


Arpeggio is provided under the GNU GPL v3.0 License.


Arpeggio was written by Alexander Ganes (


If you have any feedback for this package, please send it to
alexander.ganes (at) statgen (dot) org.

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Key Features of Arpeggio

Compute ChIP-Seq for many different TFs
Support many types of metadata
Detect known and predicted motifs
Compare two ChIP-Seq datasets in a comparative study
Easily visualize raw sequencing data and motifs


Arpeggio Requirements

Java Versions
Java 1.7+ recommended

OS Requirements


Arpeggio Architecture

It is a Java-based application that can run in two modes: command-line or GUI. The first runs as a single executable on a server with the intent to compute for multiple TFs (command-line mode). In this mode, it requires the user to pass the input via command line for processing. On the other hand, the second mode runs in a web-based GUI and receives the dataset from the user’s browser. It is able to process numerous data types in a click of a button.


The Arpeggio software is GNU/GPLv3 licensed.

The authors also suggest to apply for a license for academic research so that Arpeggio can be used freely.

Arpeggio Availability

The current stable version of Arpeggio is 1.1.0.

Preliminary 1.2.0 Development Release

Some of the key improvements in the preliminary version 1.2.0 include:

Support for tiling properties

Support for TSS/Poly-A track

Support for detecting histone mark types

Support for genome browser

Improved ChIP-seq analysis

Improved Arpeggio annotations

Multithreaded ChIP-Seq processing

New ChIP-Seq processing panel for extensive customizations

Improved RGraph

Improved VDR

Improved web server

No more required input files

Arpeggio Installation

Arpeggio can be downloaded from Arpeggio’s downloads page. After you download Arpeggio, there are some prerequisites to be installed.

Arpeggio Installation Prerequisites


RHEL7 system requirements

Red Hat Enterprise Linux 7 (GA)


Debian 7 (jessie)


CentOS 7 (jessie)

What’s New In Arpeggio?

Arpeggio is a web-based, open source software for analyzing ChIP-seq datasets from ENCODE and other projects. Arpeggio uses an efficient algorithm for mapping peak calls to the genome.
Arpeggio is a comparative analysis software for ChIP-seq peaks. Arpeggio provides several comparison modes of ChIP-seq data. In addition, Arpeggio provides a pathway based view of genomics.
Arpeggio features:

Input supporting multiple types of ChIP-seq data:

Arpeggio supports all of the ChIP-seq datasets from ENCODE.

Input-format conversion:

Arpeggio does not support input files with certain formats. Arpeggio can convert sample ids, file formats and tags to your own format (if you know how to do it).

Comparison between several datasets:

To compare several datasets, Arpeggio has peak overlap, frequency plot, and tag frequency (also called tag density) functions.

Visualization of ChIP-seq datasets:

The ChIP-seq datasets can be visualized using Arpeggio’s genome view. ChIP-seq peaks from Arpeggio can be stored in a genome browser. You can also visualize publicly available UCSC Genome Browser.

Microsfot Canvas Viewer:

Use the ChIP-seq dataset from Arpeggio with the user-friendly Canvas Viewer.

Running Arpeggio’s peak correlation analysis:

With Arpeggio, you can easily compare multiple datasets and identify features in the genome that are similar to a specific function.
Features of Arpeggio:

Arpeggio has many functions to analyze ChIP-seq data. For example, Arpeggio’s peak correlation analysis function will compare your ChIP-seq dataset against many genomes and identify comparable features.

Arpeggio ChIP-seq dataset analysis results can be stored, so if you perform similar analysis again, you can display the results together.

Reusable Arpeggio functions:

Arpeggio has a lot of functions that other software does not have. For example, you can conveniently analyze ChIP-seq data and identify similar features in the genome. To reuse the Arpeggio functions that were designed for your analysis, you can store Arpeggio

System Requirements:

OS: Windows XP/Windows 7/Windows 8 (64bit)
CPU: Intel Core 2 Duo, Intel Core 2 Quad, Intel Core 3
Hard Drive: 2 GB HD space
Display: 1024×768, 1280×1024, 1280×800, 1366×768, 1600×1200
DirectX: DirectX 9.0c
Network: Broadband Internet connection
Sound Card: DirectX-compatible
Additional Notes: The beta version for release later this month is