Genome feature and epigenomics data analysis for ChIP-Seq and ATAC-Seq experiments  
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This is a virtual workshop, you can participate by reading workshop materials, watching video presentations and carrying out exercises on an assigned BioHPC Cloud server (server assignments are listed here). If you need help, please sign up for our Office Hours. The server assigned to you for hands-on exercises will be available for a limited time, see server assignment page or bottom of this page for details. Please note, the server is assigned to you for hands-on exercises, NOT heavy computing, using the server for workshop unrelated computing is not allowed and will result in assignment termination.

This workshop covers databases and tools commonly used in epigenomics data analysis, in particular, ChIP-Seq and ATAC-Seq data analysis. The workshop will cover public genome feature annotation databases from NCBI, ENSEMBL and other community databases, commonly used genome feature file formats, genome browsers, tools for feature analysis including Homer, GREAT, Bedtools and Deeptools, and ChIP-Seq/ATAC-Seq peak calling and data QC. We assume that people who take this workshop already know how to do short-read alignment and generate bam files. Please take the genome sequence or RNA-seq data analysis workshp if you are not familiar with short read alignment.  Each workshop participant will be assigned to a Linux server, and will have three weeks to finish several data analysis projects. (Qi Sun, William Lai, Jeff Glaubitz)

Workshop videos:

Session 1
Session 3

Session 5

Workshop server assignment


Workshop Outline  
Session 1 Nov 30 2020 3:30PM - 5:00PM Zoom
Public genome feature annotation databases from NCBI and ENSEMBL; Commonly used file formats for genome feature annotation; Genome browsers including UCSC Genome Browser and IGV.
Session 2 Dec 2 2020 3:30PM - 5:00PM Zoom
Hands-on session
Session 3 Dec 7 2020 3:30PM - 5:00PM Zoom
ChIP-seq and ATAC-seq data QC and analysis, including peak calling, peak enrichment statistics agnostic to annotation features.  
Session 4 Dec 9 2020 3:30PM - 5:00PM Zoom
Hands-on session
Session 5 Dec 14 2020 3:30PM - 5:00PM Zoom
Tools for integrated analysis of genome annotation features and peak calling: Homer, GREAT, Bedtools and Deeptools.
Session 6 Dec 16 2020 3:30PM - 5:00PM Zoom
Hands-on session
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