Workshop on Analysis of ChIP-Seq Data
When: May. 16th, 2016 - May. 17th, 2016 9:30 am - 4:30 pm
To Know
About this Class
This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq Data Analysis. There will also be a talk on ENCODE and a comprehensive discussion of topics ranging from experimental design to data visualization. This workshop will include presentations on using open source applications (MACS, HOMER, MEME, SICER) as well as commercial software (Genomatix). To access the NCI Genomatix server, to request for a password through IT helpdesk to genomeanalyzer.nci.nih.gov.
NOTE: This is a BYOC (Bring your own laptop Computer) class. Government issued or personal computers are permitted. We will be able to supply a very limited set of computers, so if you want to take the class but cannot bring your own computer please indicate such in the Comment section on the registration form. This workshop will be remotely telecast to the Library Training Room in Bldg 549 at NCI-Frederick for attendees who select to register at that location. Please register only if you intend to attend the workshop.
Date: May 16-17, 2016 (Monday and Tuesday)
Time: 9:30 am – 12:30 pm and 1:30 – 4:30 pm
Locations:
Live Workshop - NIH Bethesda - Bldg 10, FAES Room 4
Remote Simulcast - NCI-Frederick - Scientific Library Training Room, Bldg 549
Workshop Agenda
Monday, May 16, 2016
Day 1 - Session 1: 9:30 am – 12:30 pm
9:30 am – 11 am
Presenter: Peter Fitzgerald, Ph.D, CCBR, OSTR, NCI
Title: Introduction to ChIP-Seq
- 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
- Reasons why Experiments Fail
- Sequence Specific Binding
- Identification of Motifs
- Overexpressed sequences
- Pathways
- Resources
- Public Repositories
- Literature References
- Software listings
11 am – 12:30 pm
Presenter: Bong-Hyun Kim, Ph.D., CCBR, Leidos Biomed
Title: Understanding ENCODE (ENCyclopedia Of DNA Elements)
- ENCODE Guidelines and best practices
- Access policies and data retrieval mechanisms
- Other public databases – Epigenome, Mouse Encode
Day 1 – Session 2
1:30 pm – 4:30 pm
Presenter: Bong-Hyun Kim, Ph.D., CCBR, Leidos Biomed
Title: ChIP-Seq Analysis Workflow
- Data QC metrics, plots and online tools
- Narrow Peak calling algorithms (e.g. MACS)
- Annotation (e.g. HOMER)
- Motif analysis (e.g. MEME)
Tuesday, May 17, 2016
Day 2 – Session 1
9:30 am –12:30 pm
Presenters: Chongzhi Zang, Ph.D., Dana-Farber Cancer Institute
Weiqun Peng, Ph.D., George Washington University
Title: Analyzing ChIP-seq data with SICER (Spatial Clustering for Identification of ChIP-Enriched Regions)
- ChIP-seq overview
- Characteristics of histone mark ChIP-seq data
- SICER algorithm: basic idea and model
- Interactive SICER tutorial (on Galaxy):
- Data format and description
- Run SICER with control
- Run SICER without control
- Run SICER for differential peak calling
- Other useful tools
Day 2 – Session 2
1:30 pm – 4:30 pm
Presenter: Susan Dombrowski, Ph.D, Genomatix
Title: Peeking into the Biology of your ChIP-Seq Peaks with Genomatix
- Automated ChIP-Seq workflow:
- Peak Calling: MACS, SICER, NGS Analyzer Read and Peak Classification Sequence Extraction Transcription Factor Binding Site Overrepresentation Motif Detection: CoreSearch
- Meta Analysis and Integration of RNA-Seq data with ChIP-Seq peaks
- Overview of RNA-Seq: Class Demo
- Positional Correlation of ChIP-Seq peaks with differentially-expressed transcripts
- Downstream Target Prediction
- Defining gene regulatory "frameworks" in co-expressed genes
Software requirements for the computer system to run Genomatix: