This workflow performs a differential expression analysis with STAR and Deseq2. It is currently under development. No stable release is available yet.
- Johannes Köster (@johanneskoester), https://koesterlab.github.io
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.
Configure the workflow according to your needs via editing the file config.yaml and the sample sheet samples.tsv.
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 or run it in a cluster environment via
snakemake --use-conda --cluster qsub --jobs 100
or
snakemake --drmaa --jobs 100
See the Snakemake documentation for further details.