This repository contains a snakemake workflow to calculate enrichment of transcription factors in cancer open chromatin regions compared to healthy open chromatin regions.
- Lea Burkard (@leaburkard)
This workflow was used with the following data:
- blood open chromatin regions: Corces et al (2016) Nat Genet. https://doi.org/10.1038/ng.3646
- cancer open chromatin regions: Corces et al (2018) Science https://doi.org/10.1126/science.aav1898
The data can be downloaded and preprocessed by exectuing the download_data.sh script.
To use this workflow transcription factor data needs to be downloaded and added to the transcriptionfactors/ folder. This worklow was designed and only used with the predicted TFBS of the JASPAR Core Collection. An instruction how to download them is written in the directory.
In the beginning of the workflow (snakefile_enriched_tf.smk) the file names for the healthy and cancer open chromatin regions need to be given without extensions. These files need to be in the input/ folder.
#### Name of healthy and cancer file ####
HEALTHY = "blood_mono_500"
CANCER = "pancancer_COAD_500"
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