example

Small Example Dataset

This dataset was derived from a real methyl-seq data (ENA PRJNA730913).

Processing this dataset takes about 10 minutes.

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Key contents

• data/panel.csv: panel of capture regions for the dataset (created by scripts/select-panel.sh)
• data/models.csv: models for testing associations in the example dataset
• data/phenotypes.csv: phenotype data for testing associations in the example dataset
• data/raw: fastq files for the example dataset (created by scripts/create-fastq-files.sh)
• data/samplesheet.csv: list of all fastq files with corresponding sample identifiers
• data/blood-cell-type-reference.csv: blood cell type DNA methylation reference dataset
• scripts/create-dataset.sh: script to recreate the example dataset
• config.yml: snakemake configuration file

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Running the pipeline

Please first edit config.yml to specify the location of your indexed hg19 genome ('paths:genome').

The entire pipeline can be applied to the dataset using the following command.

bash run-pipeline.sh

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Recreate the dataset

The dataset has already been created, so there is no need to repeat it. All outputs are contained the data/ folder.

bash scripts/create-dataset.sh PATH/TO/ORIGINAL/DATA PATH/TO/GENOME/INDEX

• PATH/TO/ORIGINAL/DATA The location where the original dataset should be (or has been) downloaded and aligned.
• PATH/TO/GENOME/INDEX The location where the human genome (hg19) should be (or has been) downloaded and indexed.