With the Snakemake pipeline in this repository, you can process scTAM-seq data for EPI-clone.
EPICloneProcessing requires the following software installations:
- conda, e.g., installed through miniforge
- snakemake
- the on-premise pipeline of Mission Bio. Please get in contact with your contact at Mission Bio to request access to the local pipeline and install it on your computer/server. This will create a conda environmet, which you will have to specify in the Snakemake file.
You'll just have to fill in the right parameters in config.yaml and then start the pipeline with:
snakemake --profile sge --jobs 1 --cluster-config cluster.yaml
This assumes that the profile sge was installed or that there is a folder called sge in the snakemake directory. For support of further compute clusters, please have a look here.
For questions, you can contact Michael Scherer.