1 ATAC-Seq Tutorial

In this tutorial we will analyze the ATAC-Seq data from this publication. The manuscript investigates the chromatin accessibility landscape of 13 human primary blood cell types. We will try to identify regulatory regions that govern hematopoietic differentiation.

1.1 Data Set

The authors kindly provided a pre-processed ATAC-Seq Count Matrix which we will use in this tutorial. If you are interested in the basic Bioinformatics methods how ATAC-Seq data is aligned to the human reference genome, quality controlled and processed for peak calling and peak annotation you can have a look at our ATAC-Seq pipeline. In this tutorial we will start with the raw count matrix of read counts per sample (columns) and peak (rows).

1.2 Prepare the input count matrix

The tutorial repository contains a shell script to download the count matrix and subset the samples to one donor.

1.3 Issues/Questions

For any question or error you may notice in the tutorial please open an issue in the GitHub tutorial repository. Thanks.