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| # Snakemake workflow: rna-seq-star-deseq2 | ||
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| [](https://snakemake.bitbucket.io) | ||
| [](https://travis-ci.org/snakemake-workflows/rna-seq-star-deseq2) | ||
| [](https://cdn.rawgit.com/snakemake-workflows/rna-seq-star-deseq2/master/.test/report.html) | ||
| [](https://snakemake.github.io) | ||
| [](https://github.com/snakemake-workflows/rna-seq-star-deseq2/actions?query=branch%3Amaster+workflow%3ATests) | ||
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| This workflow performs a differential expression analysis with STAR and Deseq2. | ||
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| ## Authors | ||
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| * Johannes Köster (@johanneskoester), https://koesterlab.github.io | ||
| * Sebastian Schmeier (@sschmeier), https://sschmeier.com | ||
| * Jose Maturana (@matrs) | ||
| This workflow performs a differential gene expression analysis with STAR and Deseq2. | ||
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| ## Usage | ||
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| ### Simple | ||
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| #### Step 1: Install workflow | ||
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| If you simply want to use this workflow, download and extract the [latest release](https://github.com/snakemake-workflows/rna-seq-star-deseq2/releases). | ||
| If you intend to modify and further extend this workflow or want to work under version control, fork this repository as outlined in [Advanced](#advanced). The latter way is recommended. | ||
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| 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). | ||
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| #### Step 2: Configure workflow | ||
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| Configure the workflow according to your needs via editing the file `config.yaml`. | ||
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| #### Step 3: Execute workflow | ||
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| Test your configuration by performing a dry-run via | ||
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| snakemake --use-conda -n | ||
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| Execute the workflow locally via | ||
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| snakemake --use-conda --cores $N | ||
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| using `$N` cores or run it in a cluster environment via | ||
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| snakemake --use-conda --cluster qsub --jobs 100 | ||
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| or | ||
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| snakemake --use-conda --drmaa --jobs 100 | ||
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| See the [Snakemake documentation](https://snakemake.readthedocs.io/en/stable/executable.html) for further details. | ||
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| If you not only want to fix the software stack but also the underlying OS, use | ||
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| snakemake --use-conda --use-singularity | ||
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| in combination with any of the modes above. | ||
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| # Step 4: Investigate results | ||
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| After successful execution, you can create a self-contained interactive HTML report with all results via: | ||
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| snakemake --report report.html | ||
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| This report can, e.g., be forwarded to your collaborators. | ||
| An example (using some trivial test data) can be seen [here](https://cdn.rawgit.com/snakemake-workflows/rna-seq-star-deseq2/master/.test/report.html). | ||
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| ### Advanced | ||
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| The following recipe provides established best practices for running and extending this workflow in a reproducible way. | ||
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| 1. [Fork](https://help.github.com/en/articles/fork-a-repo) the repo to a personal or lab account. | ||
| 2. [Clone](https://help.github.com/en/articles/cloning-a-repository) the fork to the desired working directory for the concrete project/run on your machine. | ||
| 3. [Create a new branch](https://git-scm.com/docs/gittutorial#_managing_branches) (the project-branch) within the clone and switch to it. The branch will contain any project-specific modifications (e.g. to configuration, but also to code). | ||
| 4. Modify the config, and any necessary sheets (and probably the workflow) as needed. | ||
| 5. Commit any changes and push the project-branch to your fork on github. | ||
| 6. Run the analysis. | ||
| 7. Optional: Merge back any valuable and generalizable changes to the [upstream repo](https://github.com/snakemake-workflows/rna-seq-star-deseq2) via a [**pull request**](https://help.github.com/en/articles/creating-a-pull-request). This would be **greatly appreciated**. | ||
| 8. Optional: Push results (plots/tables) to the remote branch on your fork. | ||
| 9. Optional: Create a self-contained workflow archive for publication along with the paper (snakemake --archive). | ||
| 10. Optional: Delete the local clone/workdir to free space. | ||
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| ## Testing | ||
| The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=snakemake-workflows%2Frna-seq-star-deseq2). | ||
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| Tests cases are in the subfolder `.test`. They are automtically executed via continuous integration with Travis CI. | ||
| If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this (original) repository and its DOI (see above). |