This is a tutorial to analyze an ATAC-Seq count matrix as produced by our ATAC-Seq pipeline. The command requires R Statistics and a number of additional R packages. To install R and the dependent packages just execute:
make install
If you already have R installed or want to install the packages manually just skip this step.
To download the tutorial data and subset to a small number of samples.
./preprocess.sh
This step produces the sample information table blood.samples and the actual count data atac.data.gz, which are required input files for the tutorial.
You can build the ATAC-Seq book in HTML using
make book
You can then browse the tutorial content using
firefox _book/index.html
The online version of these HTML files you can find here
You can convert the Rmarkdown file to a standard Rscript file using
make atac
This tutorial was created with contributions from Markus Hsi-Yang Fritz.