Bioinformatics Training and Education Program

ChIP-Seq Data Analysis Workshop (2-day)

ChIP-Seq Data Analysis Workshop (2-day)

 When: Nov. 18th, 2014 - Nov. 19th, 2014 9:30 am - 4:30 pm

To Know

FAES Classroom 4
Presented By:
Peter FitzGerald (GAU)
Class Files:
This class has ended.

About this Class

Day 1 - AM (9:30-12:30)  Introductory Lecture
(Peter FitzGerald, PhD - CCR, NCI)

  • Introduction
    • Historical Perspective and Technical Variations
    • Experimental methodology
    • Comparison to ChIP-Chip
  • Data Analysis
    • Experimental Design
    • Quality Control 
    • Peak Calling (Different methodologies)
    • Major Sources of Error
    • Causes of Fail Experiments
    • Validation Methods
  • Sequence Specific Binding
    • Identification of Motifs
    • Overexpressed sequences
    • Pathways
  • Resources
    • Public Repositories
    • Literature References
    • Software listings

Day 1 - PM  (1:30-4:30)  Introduction to Genomatix
The Genomatix Mining Stations (GMS) and the Genomatix Genome Analyzer (GGA) at the NCI
(Susan Dombrowski, PhD - Genomatix)

  • The basics of these tools
  • Importing data and mapping of NGS data on the GMS

Day 2 - AM (9:30-12:30)  Genomatix Continued
(Susan Dombrowski, PhD - Genomatix)

  • Import of data to the GGA
  • Automated, Complete Workflow for ChIP-Seq Analysis
    • Peak Finding
    • Read and Peak Classification
    • Sequence Extraction
    • TFBS overrepresenation
    • Definition of new TFBS
  • Downstream Application Areas
    • Position Correlation with ENCODE ChIP-Seq data
    • Annotation of binding regions: target prediction
    • Pathway analysis of potential TF targets
Day 2 - PM (1:30-4:30)  ChIP-Seq data analysis and integration using Cistrome
(Chongzhi/George Zang, PhD - Dana-Farber Cancer Institute, Harvard School of Public Health)

Cistrome ( is a web-based platform for ChIP-chip and ChIP-seq data analysis and integration. “Cistrome” refers to the in vivo genome-wide location of a transcription factor or a histone modification, which can be characterized using ChIP-chip or ChIP-seq. In this training session, I will introduce the basic functions of Cistrome analysis pipeline and the recently launched Cistrome dataset browser, which has collected over 12,000 public ChIP-seq datasets. Then I will give a practical example to analyze a ChIP-seq dataset using a series of tools on Cistrome. The practice will include: 


  • ChIP-seq peak calling using MACS
  • ChIP-seq integrative analyses
  • ChIP-seq and gene expression data integration using BETA
  • Investigate public ChIP-seq data using Cistrome Dataset Browser 

UCSC Demo lnks

USCS-with data hub

Helix-with data hub


  • Cistrome_Training_20141119.pdf: |
  • Final_ChipSeq20_2014.pdf: |
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  • NCI_GGA_updated2.docx: |
  • NCI_GMS.docx: |
  • NCI_0914.pdf: |