Genome feature and epigenomics data analysis for ChIP-Seq and ATAC-Seq experiments  
November 30 - December 16 2020

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)

Recordings from this workshop are available online (restricted to workshop participants only).

Machine allocation.

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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