Skip to content

callpeak_ATACseq.smk

Snakemake workflow for peak calling of ATAC-seq data.

Note

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

Workflow

callpeak_ATACseq.smk rulegraph

The rulegraph was created by snakevision.

  1. Peak calling using MACS with the parameter specified in the config.yaml.
  2. Make summary statistics using MultiQC.

Usage

1
2
3
4
5
snakemake -s /path/to/SnakeNgs/snakefile/callpeak_ATACseq.smk \
--configfile /path/to/config.yaml \
--cores <int> \
--use-singularity \
--rerun-incomplete

config.yaml should contain the following information:

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
# general
workdir: /path/to/output
samples: ["SRRXXXXXX", "SRRYYYYYY", "SRRZZZZZZ"]

# macs2
broad: False # Boolean
broad_cutoff: # Float when broad is True
genomesize: hs # ["hs", "mm", "ce", "dm"]
fileformat: BAMPE # ["BED", "BAM", "SAM", "BEDPE", "BAMPE"]
qvalue: 0.05
  • path/to/output should contain fastq directory with the following structure:
1
2
3
4
5
output/
└── bowtie2
    ├── SRRXXXXXX.sort.rmdup.bam
    ├── SRRYYYYYY.sort.rmdup.bam
    └── SRRZZZZZZ.sort.rmdup.bam

Is is expected that the input BAM files are generated by the preprocessing_ChIPseq.smk workflow.

  • 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