Basics of ChIP-seq analysis - how to explore this kind of data

Offered by:LuciLinX with Merja Heinäniemi
When:24 + 25 November 2011
Where:University of Luxembourg, Bâtiment des Sciences, Room BS 0.11
Duration:1 pm - 5 pm
Requirements:See info about day 2
Restrictions:Maximum 20 participants. First-come first-serve
Registration:By email to Merja Heinäniemi
Contact:merja DOT heinaniemi AT uni DOT lu

Description of Day 1, 24 November

Target audience: mainly biologists, no command line skills required, no raw data analysis

How to use (ChIP-)seq datasets?

  1. Introduction to biology: genes, transcription factors and histone markers
  2. Finding transcription factor binding sites and enhancers using ChIP-seq data
  3. GEO and data formats
  4. ENCODE data


  1. Downloading peak data
  2. Visualization of ChIP-seq data
  3. Using Galaxy to convert formats, find overlapping regions, retrieve fasta sequences etc

Description of Day 2, 25 November

Target audience: bioinformaticians, command line skills required, raw data analysis (in the limits of available CPU / RAM resources)

How to analyze (ChIP-)seq datasets?

  1. 1. Fastq and solexa format
  2. Taq alignment options
  3. Taq shifting for peak detection
  4. Statistics of peak detection


  • Downloading raw ChIP-seq data
  • Alignment of reads
  • Quality control
  • Peak detection
  • Enrichment analysis

  • Requirements

    As analysis of raw (Chip-)seq data requires long run-times and a lot of space and memory, the practicals will be more demonstration than really hands-on experience. However, participants are encouraged to bring their own (large) external harddisks, if available, to get the software + files to later test them at their own computer (assuming that meets software requirements).

    If possible, please bring a laptop with a Linux installation, or with Linux installed in a VirtualBox environment. If you need help with this, please contact Anke Wienecke "anke dot wienecke at uni dot lu" who can guide you through the installation.