Snakemake Workflow for ATAC-Seq

A snakefile pipeline for ATAC-Seq.

Change the config.yaml file appropriately according to your data. Update replicate1.tsv and replicate2.tsv for Replicates 1 and Replicates 2 respectively. Update parameters of Genrich in the config file.

Then run: snakemake -jnumber_of_cores, for example for 5 cores use:

snakemake -j5

and for a dry run use:

snakemake -j1 -n

and to print the commands in a dry run use:

snakemake -j1 -n -p

To use another config file use:

snakemake -j1 -p --configfile configfilehere.yaml

For the sake reproducibility, use conda to pull same versions of tools. Snakemake and conda have to be installed in your system:

snakemake --cores --use-conda

Citation

If you use this pipeline, please cite us as follows:

Sherine Awad. (2022). SherineAwad/ATAC-Seq: v1.0.0 (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.5939988