ATAC-seq / ChIP-seq / Open Chromatin pipeline

February 2021: The repository structure and version keeping has been changed. There are no longer "stable" and "dev" folders for the stable and development versions, respectively. I switched to proper Git branches and the repository in m projects folder may contain the files from either of the branches.

The default master branch hosts the code for the stable version of the pipeline.

If you want to use the pipeline, please follow the following easy instructions:

1. Clone the repository and switch to the branch you want to use. This will almost always be the "stable" version from the master branch, in which case NOTHING has to be done - you already have, by default, the master branch of the repository. git clone git@git.embl.de:carnold/ATACSeq_Snakemake.git. To see all available branches, type "git branch -a". You should see that the master branch is already the currently active branch
2. Use the examples/templates folder to quickly get started with examples for the genome of your choice and prepare your dataset. In addition, you can check the examples/input folder.
3. Run the pipeline.

For parameter explanation, see the explanations in the config yaml files.

There are some important changes that were introduced with the most recent version. Make sure to read the config.yaml and ask Christian in case of open questions. In short, some parameters and parts of the pipeline have been deprecated (Encode peak calling), default paramters have changed (e.g., no RSS adjustment is done anymore by default, but this can be changed).

If you are not familiar with Snakemake and how to run our pipelines, make sure to check the doc folder and the linked PDF therein (it is a symbolic link to the file /g/scb/zaugg/zaugg_shared/scripts/Christian/doc/Snakemake/Snakemake - How to run my pipelines.pdf')