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Introduction

This tutorial introduces the basic principles of analyzing chromatin immunoprecipitation sequencing (ChIP-seq) data and is intended to provide enough information to perform key steps of ChIP-seq analysis: quality control of data, mapping data to a reference genome and peak calling. We will be using Cyverse discovery environment public apps for analysis of a sample set. Command-line expertise is not required to follow most of this tutorial.

Learning Objectives

  • Efficiently manage and analyze ChIP-seq data
  • How to do quality assessment using ChIPQC R package
  • Using CyVerse Discovery Environment apps to do ChIP-seq analysis


Manual Maintainer(s)

Who to contact if this manual needs fixing. You can also email Tutorials@CyVerse.org

Maintainer Institution Contact
Reetu Tuteja CyVerse / UA reetututeja@cyverse.org

Note

Acknowledgments: Thanks to VIB and Harvard Chan Bioinformatics training for making wonderful teaching material available for ChIP-seq.

Prerequisites

Downloads, access, and services

In order to complete this tutorial you will need access to the following services/software

Prerequisite Preparation/Notes Link/Download
CyVerse account You will need a CyVerse account to complete this exercise CyVerse User Portal
Cyberduck Standalone software for upload/download to Data Store Download Cyberduck

Platform(s)

We will use the following CyVerse platform(s):

Platform Interface Link Platform Documentation Quick Start
Data Store GUI/Command line Data Store Data Store Manual Data Store Guide
Discovery Environment Web/Point-and-click Discovery Environment DE Manual Discovery Environment Guide

Application(s) used

Discovery Environment App(s):

App name Version Description App link Notes/other links
Bowtie 1.2.2 Short-read sequence aligner DE Application URL Original App Documentation
FastQC 0.11.5 Quality Control tool for HTS data DE Application URL Original App Documentation
MACS2 2.7.1 Model-based analysis of ChIP-seq DE Application URL Original App Documentation
ChIPQC 1.22 Quality assessment tool for ChIP-seq DE Application URL Original App Documentation

Input and example data

In order to complete this tutorial you will need to have the following inputs prepared

Input File(s) Format Preparation/Notes Example Data
ChIP-seq experiment data fastq or sra files Data downloaded from GEO or ENA database Myers et al., 2013 FNR dataset (iplantcollaborative > example_data > chipseq_webinar)

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