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

2. Clone the repo

git clone https://github.com/lacklab/MuSTARRd.git
cd MuSTARRd

3. Modify config/config.yaml, config/samples.tsv and config/units.tsv (see here)
4. Run the snakemake workflow with the following:

snakemake --profile profile/ # use your own profile - modify profile/config.yaml

Documentation is a WIP