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callpeak_ChIPseq.smk

Snakemake workflow for peak calling of ChIP-seq data.

Note

Please make sure that you have Singularity and Snakemake installed on your system and cloned the SnakeNgs repository.

Workflow

callpeak_ChIPseq.smk rulegraph

The rulegraph was created by snakevision.

  1. Peak calling using MACS with the parameter specified in the config.yaml.
  2. Convert bedgraph files to bigwig files using bedgraphtobigwig.
  3. Make summary statistics using MultiQC.

Usage

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snakemake -s /path/to/SnakeNgs/snakefile/callpeak_ChIPseq.smk \
--configfile /path/to/config.yaml \
--cores <int> \
--use-singularity \
--rerun-incomplete

config.yaml should contain the following information:

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general:
  workdir: /path/to/output
  experiment_table: /path/to/experiment_table.tsv

macs2:
  broad: False # Boolean
  broad_cutoff: # Float when broad is True
  genomesize: hs # ["hs", "mm", "ce", "dm"]
  fileformat: BAM # ["BED", "BAM", "SAM", "BEDPE", "BAMPE"]
  qvalue: 0.05

bedgraphtobigwig:
  assembly: hg38
  • experiment_table.tsv should contain the following information:
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sample  target  control
sample1 /path/to/sample1_target.bam /path/to/control_A.bam
sample2 /path/to/sample2_target.bam /path/to/control_B.bam
sample3 /path/to/sample3_target.bam /path/to/control_A.bam

target and control are paths to the BAM files for the target and control (input) samples, respectively.

  • macs2 contains the parameters for MACS2 peak calling. Please refer to the MACS2 documentation.

  • bedgraphtobigwig contains the assembly information for the conversion of bedgraph files to bigwig files.

Docker image used in the workflow