Code to process raw SNARE-seq ATAC reads
MIT License
Code to process raw SNARE-seq ATAC reads for the adult mouse brain.
Steps:
The pipeline is constructed using snakemake. To run the pipeline, first install miniconda, then create a conda environment for the pipeline using the environment.yaml file. This will install all the dependencies needed:
conda env create -f environment.yaml
This creates an environment called snareseq
. Activate this environment when running the
pipeline: conda activate snareseq
.
You can execute a dry-run of the pipeline to see what steps will be run using:
snakemake -n
To run the pipeline and generate the outputs, run:
snakemake --cores 8
Note that this involves >500 Gb of raw data.
Overview of the pipeline: