RNA-seq workflow using STAR and DESeq2
This workflow performs a differential expression analysis with STAR and Deseq2.
If you simply want to use this workflow, download and extract the latest release. If you intend to modify and further extend this workflow or want to work under version control, fork this repository as outlined in Advanced. The latter way is recommended.
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, if available, its DOI (see above).
Configure the workflow according to your needs via editing the file
Test your configuration by performing a dry-run via
snakemake --use-conda -n
Execute the workflow locally via
snakemake --use-conda --cores $N
$Ncores or run it in a cluster environment via
snakemake --use-conda --cluster qsub --jobs 100
snakemake --use-conda --drmaa --jobs 100
See the Snakemake documentation for further 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.
After successful execution, you can create a self-contained interactive HTML report with all results via:
snakemake --report report.html
This report can, e.g., be forwarded to your collaborators. An example (using some trivial test data) can be seen here.
The following recipe provides established best practices for running and extending this workflow in a reproducible way.
Tests cases are in the subfolder
.test. They are automtically executed via continuous integration with Travis CI.