HOMER GETDIFFERENTIALPEAKS

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Detect differentially bound ChIP peaks between samples. For more information, please see the documentation.

Example

This wrapper can be used in the following way:

rule homer_getDifferentialPeaks:
    input:
        # peak/bed file to be tested
        peaks="{sample}.peaks.bed",
        # tagDirectory of first sample
        first="tagDir/{sample}",
        # tagDirectory of sample to compare
        second="tagDir/second"
    output:
        "{sample}_diffPeaks.txt"
    params:
        extra=""  # optional params, see homer manual
    log:
        "logs/diffPeaks/{sample}.log"
    wrapper:
        "v3.4.1/bio/homer/getDifferentialPeaks"

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.

Software dependencies

  • homer=4.11

Authors

  • Jan Forster

Code

__author__ = "Jan Forster"
__copyright__ = "Copyright 2020, Jan Forster"
__email__ = "j.forster@dkfz.de"
__license__ = "MIT"

from snakemake.shell import shell
import os.path as path
import sys

extra = snakemake.params.get("extra", "")
log = snakemake.log_fmt_shell(stdout=True, stderr=True)

shell(
    "(getDifferentialPeaks"
    " {snakemake.input.peaks}"
    " {snakemake.input.first}"
    " {snakemake.input.second}"
    " {extra}"
    " > {snakemake.output})"
    " {log}"
)