Analysis of ATAC-seq data in R/Bioconductor

The use of ChIP-seq, DNA-seq and MNAse-seq to identify transcription factor binding, open chromatin and nucleosome positions respectively has led to a broader understanding of epigenetic events across the genome. ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput sequencing) offers a method to rapidly and simultaneously identify openchromatin, nucleosome positioning and transcription factor binding at a genome scale. In this session, we will review the alignment, pre-processing and peak calling of ATAC-seq data in R/Bioconductor and will perform quality control, identification of replicated peaks, annotation of peaks to genes and visualization of ATAC-seq data in IGV.

This session will be presented by Thomas S. Carroll, Ph.D., head of Bioinformatics at The Rockefeller University.

Run these two lines of code in R to prepare:

# install required packages (and Bioconductor if needed)
source("https://gist.githubusercontent.com/lwaldron/220828bae0764a80fcf3a23868bf182e/raw/b30211484ac59eb0bf833b1d9ed507d65449134d/installpkgs.R")

# download essential files to present working directory
source("https://gist.githubusercontent.com/lwaldron/c1e44d0516422777e3f87d6726d45332/raw/674a67d52e862442c17a1f8ee17f47c401bf7b09/downloadessentials.R")