Commit 0f74a8bf authored by Sarah Peter's avatar Sarah Peter

References and link to snakemake tutorial

parent 715017db
......@@ -123,7 +123,7 @@ Create a working directory and link the necessary data:
> ```
> &mdash; <cite>[Snakemake manual - Rules](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html)</cite>
For a detailed explanation of rules, have a look at the official [Snakemake tutorial](https://snakemake.readthedocs.io/en/stable/tutorial/basics.html).
A basic rule for mapping a fastq file with [bowtie2](http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) could look like this:
......@@ -607,6 +607,15 @@ With `squeue -u <your_username>` you can check the status of the submitted jobs
## References
* [Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.](http://bioinformatics.oxfordjournals.org/content/28/19/2520)
* [Gérard D, Schmidt F, Ginolhac A, Schmitz M, Halder R, Ebert P, Schulz MH, Sauter T, Sinkkonen L. Temporal enhancer profiling of parallel lineages identifies AHR and GLIS1 as regulators of mesenchymal multipotency. *Nucleic Acids Research*, Volume 47, Issue 3, 20 February 2019, Pages 1141–1163, https://doi.org/10.1093/nar/gky1240](https://www.ncbi.nlm.nih.gov/pubmed/30544251)
* [Langmead B, Salzberg S. Fast gapped-read alignment with Bowtie 2. *Nature Methods*. 2012, 9:357-359.](http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1923.html)
* [Zhang et al. Model-based Analysis of ChIP-Seq (MACS). *Genome Biol* (2008) vol. 9 (9) pp. R137](http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=18798982%5Bpmid%5D)
## Acknowledgements
Many thanks to Aurélien Ginolhac, Cedric Laczny, Nikola de Lange and Roland Krause for their help in developing this tutorial.
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