west-rynes / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

Snakemake workflow: rna-seq-star-deseq2

This workflow performs a differential expression analysis with STAR and Deseq2.

Authors

• Johannes Köster (@johanneskoester), https://koesterlab.github.io

Usage

Step 1: Install workflow

If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further develop this workflow, fork this reposity. Please consider providing any generally applicable modifications via a pull request.

In any case, if you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository and, once available, its DOI.

Step 2: Configure workflow

Configure the workflow according to your needs via editing the file config.yaml and the sheets samples.tsv and units.tsv.

Step 3: Execute workflow

All you need to execute this workflow is to install Snakemake via the Conda package manager. Software needed by this workflow is automatically deployed into isolated environments by Snakemake.

Test your configuration by performing a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

using $N cores. Alternatively, it can be run in cluster or cloud environments (see the docs for details).

If you not only want to fix the software stack but also the underlying OS, use

snakemake --use-conda --use-singularity

in combination with any of the modes above.

Step 4: Investigate results

After successful execution, you can create a self-contained report with all results via:

snakemake --report report.html