The International Regulome Consortium hosted the OHRI Workshop on Next Generation Sequencing and ChIP-Seq Data Analysis on March 30, 2010 at the Sprott Center for Stem Cell Research.

Presentations and relavant links for the afternoon ChIP-Seq tutorial session are provided here:

Part 1: Quality

• Presentation (PDF)

Part 2: Visualization

• Presentation (PDF)

Genome browsers

• UCSC Genome Browser
• Ensembl
• GBrowse
• JBrowse
• Integrated Genome Browser
• Integrative Genomics Viewer

File conversion

• Samtools
  

Example files

Coming soon - watch this space

Part 3: Peak Calling

• Presentation (PDF)

Paper outlining ChIP-seq analysis approaches and tools

• Pepke et al. Computation for ChIP-seq and RNA-seq studies. Nat Meth (2009) vol. 6 (11 Suppl) pp. S22-32

Links to the ChIP-seq tools mentioned in the presentation

• GLITR
• MACS
• PeakSeq
• spp

Part 4: Data Integration

• Presentation (PDF)
• R analysis tutorial (PDF)