EPIC

Find broad enriched domains in ChIP-Seq data with epic

Example

This wrapper can be used in the following way:

rule epic:
    input:
      treatment = "bed/test.bed",
      background = "bed/control.bed"
    output:
      enriched_regions = "epic/enriched_regions.csv", # required
      bed = "epic/enriched_regions.bed", # optional
      matrix = "epic/matrix.gz" # optional
    log:
        "logs/epic/epic.log"
    params:
      genome = "hg19", # optional, default hg19
      extra="-g 3 -w 200" # "--bigwig epic/bigwigs"
    threads: 1 # optional, defaults to 1
    wrapper:
        "v5.2.1/bio/epic/peaks"

Note that input, output and log file paths can be chosen freely.

When running with

snakemake --use-conda

the software dependencies will be automatically deployed into an isolated environment before execution.

Notes

• All/any of the different bigwig options must be given as extra parameters

Software dependencies

• epic=0.2.12

• pandas=1.1.5

Input/Output

Input:

• treatment: chip .bed(.gz/.bz) files

• background: input .bed(.gz/.bz) files

Output:

• enriched_regions: main output file with enriched peaks

• bed: (optional) contains much of the same info as enriched_regions but in a bed format, suitable for viewing in the UCSC genome browser or downstream use with bedtools

• matrix: (optional) a gzipped matrix of read counts

Params

• extra: additional parameters

• log: (optional) file to write the log output to

Authors

• Endre Bakken Stovner

Code

__author__ = "Endre Bakken Stovner"
__copyright__ = "Copyright 2017, Endre Bakken Stovner"
__email__ = "endrebak85@gmail.com"
__license__ = "MIT"


from snakemake.shell import shell

# Placeholder for optional parameters
extra = snakemake.params.get("extra", "")
threads = snakemake.threads or 1

treatment = snakemake.input.get("treatment")
background = snakemake.input.get("background")

# Executed shell command
enriched_regions = snakemake.output.get("enriched_regions")

bed = snakemake.output.get("bed")
matrix = snakemake.output.get("matrix")

if len(snakemake.log) > 0:
    log = snakemake.log[0]

genome = snakemake.params.get("genome")

cmd = "epic -cpu {threads} -t {treatment} -c {background} -o {enriched_regions} -gn {genome}"

if bed:
    cmd += " -b {bed}"
if matrix:
    cmd += " -sm {matrix}"
if log:
    cmd += " -l {log}"

cmd += " {extra}"

shell(cmd)