Create a Computing Environment

Our ATAC-seq data analysis will involve many pieces of interlinking software, all of which have their own versions and dependencies. To ensure this software meshes appropriately, we need a package management system. This tutorial will use Conda – an open-source package and environment management system that runs on every major operating system.

Conda lets us effortlessly install and manage the necessary software and dependencies in a so-called “environment,” which ensures reproducibility of the results. Specifically, we’ll employ Miniconda, which is a free, minimal Conda installer.

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Download Miniconda here.

After you’ve downloaded and installed Conda, we’ll need to create environments where all the necessary software will reside. There are two ways to do this:

Option A: Manually create an environment (recommended)

From your command-line interface (i.e. terminal), run the following command to create an empty environment called “atacseq”:

conda create -n atacseq

Now run this command to activate the environment:

conda activate atacseq

Next, install the required packages to your atacseq environment with the following commands:

conda install -c bioconda macs2 
conda install -c bioconda fastqc
conda install -c bioconda multiqc
conda install -c bioconda bwa
conda install -c bioconda picards
conda install -c bioconda samtools
conda install -c bioconda bedtools
conda install -c bioconda igv

Now create and activate the diffbind environment:

conda create -n diffbind
conda activate diffbind

Finally, install DiffBind Bioconductor package to the diffbind environment

conda install -c bioconda bioconductor-diffbind

Option B: Load a pre-built environment from a yml file

Alternatively, you can install a pre-made environment from a yml file using a single command. We’ve created a yml file (for Linux and Mac operating systems) that contains all software necessary for this tutorial.

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Download the yml file here.

After downloading, simply run:

 conda env create -n atacseq --file atacseq.yml

That’s it! You now have a fully functional computing environment for the ATAC-seq analysis.