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preprocessing_ChIPseq.smk

Snakemake workflow for preprocessing paired-end and single-end ChIP-seq/ATAC-seq data. The layout parameter in the config file controls the mode.

Note

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

Workflow

Paired-end (layout: "paired")

preprocessing_ChIPseq.smk rulegraph

The rulegraph was created by snakevision.

  1. Quality control using fastp with the default parameters.
  2. Alignment using Bowtie2 with the parameter specified in the config.yaml.
  3. Convert the SAM file to BAM file and sort using samtools.
  4. Remove duplicates using Picard MarkDuplicates with the parameter --REMOVE_DUPLICATES true.
  5. Collect metrics using Picard CollectInsertSizeMetrics.
  6. Make fingerprint plots using deepTools plotFingerprint with the parameter --minMappingQuality 30 --skipZeros --numberOfSamples 50000 --binSize 10000.
  7. Make bigWig files using deepTools bamCoverage with the parameter --binSize 1 --normalizeUsing CPM.
  8. Make summary statistics using MultiQC.

Single-end (layout: "single")

preprocessing_ChIPseq_single.smk rulegraph

The rulegraph was created by snakevision.

  1. Quality control using fastp with the default parameters.
  2. Alignment using Bowtie2 with the parameter specified in the config.yaml.
  3. Convert the SAM file to BAM file and sort using samtools.
  4. Remove duplicates using Picard MarkDuplicates with the parameter --REMOVE_DUPLICATES true.
  5. Make fingerprint plots using deepTools plotFingerprint with the parameter --minMappingQuality 30 --skipZeros --numberOfSamples 50000 --binSize 10000.
  6. Make bigWig files using deepTools bamCoverage with the parameter --binSize 1 --normalizeUsing CPM.
  7. Make summary statistics using MultiQC.

Usage

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

config.yaml should contain the following information:

Paired-end

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workdir: path/to/output
samples: ["SRRXXXXXX", "SRRYYYYYY", "SRRZZZZZZ"]
bowtie2_index: path/to/bowtie2_index
bowtie2_args: ""
layout: "paired"
  • path/to/output should contain fastq directory with the following structure:
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output/
└── fastq
    ├── SRRXXXXXX_1.fastq.gz
    ├── SRRXXXXXX_2.fastq.gz
    ├── SRRYYYYYY_1.fastq.gz
    ├── SRRYYYYYY_2.fastq.gz
    ├── SRRZZZZZZ_1.fastq.gz
    └── SRRZZZZZZ_2.fastq.gz

Single-end

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workdir: path/to/output
samples: ["SRRXXXXXX", "SRRYYYYYY", "SRRZZZZZZ"]
bowtie2_index: path/to/bowtie2_index
bowtie2_args: ""
layout: "single"
  • path/to/output should contain fastq directory with the following structure:
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output/
└── fastq
    ├── SRRXXXXXX.fastq.gz
    ├── SRRYYYYYY.fastq.gz
    └── SRRZZZZZZ.fastq.gz

Common settings

  • bowtie2_args is the optional argument for Bowtie2 (e.g., --very-sensitive).

Please refer to the tutorial for more information.

Docker image used in the workflow