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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