Olivier Elemento

ChIPseeqer

ChIPseeqer is a comprehensive software package for analysis of ChIP-seq data, developed in the Elemento lab with input from the Melnick and Campagne labs at WCMC. It is designed to run on a standard desktop or laptop running Linux, Max OS X or Windows/Cygwin.

ChIP-seq is a high-throughput sequencing-based technique to determine where in the genome a particular protein binds, in a given cell type and/or condition. The Elemento and Melnick labs are now routinely using ChIPseeqer to analyze binding of several transcription factors and histone modifications.

The ChIPseeqer package contains several tools that allows the user to perform different types of analyses to ChIP-seq data:

Analysis 1: Peak detection
ChIPseeqer is a fast and accurate program for detecting ChIP-seq peaks. Using ChIPseeqer one can analyze ChIP-seq datasets with or without INPUT data. It also supports a variety of read file formats: bed, eland and mit (see Supported Formats).

Analysis 2: Visualization of peak locations in UCSC Genome Browser
ChIPseeqer2Track is a tool that creates UCSC Genome Browser tracks (WIGL) for the detected peaks.

Analysis 3: Search for regulatory elements using FIRE
ChIPseeqer2FIRE is a tool used to interface ChIP-seeqer target regions with our FIRE regulatory element discovery program.

Analysis 4: Determine pathways associated with genes using iPAGE
ChIPseeqer2iPAGE is a tool that associated the detected ChIPseeqer peaks with human RefSeq promoters and allows running pathway analyses using iPAGE.

Analysis 5: Evaluate conservation of detected peaks
ChIPseeqer2Cons is a tool that evaluates the cross-species conservation of the regions under the peaks.

The software package also includes:

ChIPfinder, which returns the maximum read count (maximum peak height) in a given set of genomic regions

CompareIntervals, a nifty multi-purpose genomic interval comparison tool (e.g. can be used to examine overlap between CpG islands and genomic targets of TF, or to determine which miRNAs have ChIP-seq peaks nearby)

CompareGenes, a tool that allows finding the common genes (some of the detected peaks where found in their promoters) between two different ChIP-seq runs.

Installation

For a detailed installation guide of ChIPseeqer visit this link.

Tutorial

A comprehensive tutorial on how to use the ChIPseeqer tools to analyze ChIP-seq data is provided here.