ChIP-Seq NGS Data Analysis

Instructor: Chitra Kotwaliwale (

March 18, 2013


A widely-used, fast, robust ChIP-seq peak-finding algorithm.

A ChIP-seq peak calling algorithm, implemented as an R package.

An open, web-based platform with some useful tools for ChIP-Seq data analysis.

The Cistrome AP module organizes analysis tools in a pipeline for users, and provides users a dry-lab workbench for them to process their own private data.

Relevant papers:
This paper discusses GC and other biases in high-througput sequencing
Paper by Liu and colleagues describing MACS
Detailed "protocol" for how to install and use MACS
ChIP-Seq guidles outlined by ENCODE and modENCODE
Paper by Kharchenko and colleagues describing spp

Useful Links:
Information about file formats