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Analysis of Saturation Mutagenesis STARR-seq data

Running the pipeline

  1. Install Snakemake
mamba create -c bioconda -c conda-forge -n snakemake snakemake
conda activate snakemake
  1. Clone the repo
git clone https://github.com/lacklab/MuSTARRd.git
cd MuSTARRd
  1. Modify config/config.yaml, config/samples.tsv and config/units.tsv (see here)
  2. Run the snakemake workflow with the following:
snakemake --profile profile/ # use your own profile - modify profile/config.yaml

Documentation is a WIP