README.md

Dependencies:

• Local installation of snakemake (see website for instructions)
• python
• bismark/0.14.5
• bedtools/2.25.0
• samtools/1.3.1

Execution: bash ProcessRRBSLauncher.sh --argument value --flag

Required arguments: -f/--fastq: Path to directory containing unzipped fastq files of the following format: <pool_prefix>_R1_001.fastq and <pool_prefix>_R2_001.fastq -g/--genome: Path to bismark-compatible genome -p/--pipeline: Path to directory containing pipeline (ProcessRRBS.mk) and other scripts -t/--target: Target of pipeline (See potential values below)

Potential Values of target argument (in reverse order of execution): -by_region: execute full pipeline and create region by cell matrix (requires optional regions argument below) -sites_only: execute full pipeline up to site by cell matrix creation -bismark_extract: execute pipeline up to bismark methylation extraction -bismark_align: execute pipeline up to bismark alignment -demultiplex: execute pipeline up to demultiplexing of fastq files

Optional arguments: -r/--regions: Bed file containing genomic regions to analyze (required if target specified as 'by_region') -c/--cluster-conifg: path to config file if submitting to cluster (see examples in this directory)

Optional flags: --qsub: submit underlying jobs to cluster (requires cluster configuration file provided to -c argument) --dry-run: map out pipeline but do not execute --dag: create directed acyclic graph representing pipeline