Epigenomics Workshop


In November 2017, COBRE Functional Genomics and SC INBRE Bioinformatics Core hosted a workshop focused on Epigenomics profiling and Functional analysis of the results (see program below). The workshop was conducted by Drs. Yurii Chinenov and David Oliver (The David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery and Weil Cornell Medicine).

The first session provided an overview of the technologies and analysis and the second session provided hands-on training of R-based analysis tools. Materials from Day 1 are linked below.

Organizers: Drs. Michael Shtutman and Homayoun Valafar


CHIP-seq and ATAC-seq for Epigenomics Profiling and Functional Analysis

Thursday, November 16th, 2 pm – 6 pm (Day 1)

1. Introduction to Epigenomics profiling.
2. Analysis of CHIP-seq and ATAC-seq data:

  • experimental design and analytical pipelines
  • quality control: before peak calling
  • peak calling
  • quality controls: after peak calling
  • peak annotation

3. Functional analysis with public tools

Click here to view CHIP-seq materials, presented by Dr. Yurii Chinenov (on Github)
Click here to view ATAC-seq materials, presented by Dr. David Oliver (on Github)

Friday, November 17th, 2 pm -6 pm (Day 2)
R proficiency is required for the second-day session. Up to 12 participants.

1. Chip-Seq/Atac-Seq data analysis with R
2. Quality control, peak annotation and functional profiling with R