A Snakemake workflow for calculating codon usage on coding sequences, including the RSCU (relative synonymous codon usage), currently restricted to the human genome (see the config/README.md for more details).
The usage of this workflow is described in the Snakemake Workflow Catalog. This includes a visualization of the workflow diagram and a table with all workflow parameters.
Detailed information about input data and workflow configuration can also be found in the config/README.md.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or its DOI.
To run the workflow from command line, change the working directory.
cd path/to/snakemake-workflow-nameAdjust options in the default config file config/config.yaml.
Before running the complete workflow, you can perform a dry run using:
snakemake --dry-runTo run the workflow with test files using conda:
snakemake --cores 2 --sdm conda --directory .testThe profiles/ directory can contain any number of workflow-specific profiles that users can choose from.
The profiles README.md provides more details.
- David Lähnemann
- German Cancer Consortium (DKTK), partner site Essen-Düsseldorf, A partnership between DKFZ and University Hospital Essen
- https://orcid.org/0000-0002-9138-4112
- Muhammad Murad
- German Cancer Consortium (DKTK), partner site Essen-Düsseldorf, A partnership between DKFZ and University Hospital Essen
- https://orcid.org/0000-0001-6030-5672
Sharp, P. M.; Tuohy, T. M. F.; Mosurski, K. R. Codon Usage in Yeast: Cluster Analysis Clearly Differentiates Highly and Lowly Expressed Genes. Nucleic Acids Res 1986, 14 (13), 5125–5143. https://doi.org/10.1093/nar/14.13.5125
Köster, J., Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., & Nahnsen, S. Sustainable data analysis with Snakemake. F1000Research, 10:33, 10, 33, 2021. https://doi.org/10.12688/f1000research.29032.2.