ATAC-Seq Data Analysis Workflow with Snakemake and Conda Environment

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ATAC-seq workflow.

Mohamed Malek CHAOUCHI

Université Clermont auvergne, 2021

Dependencies, in order of use: 

	- FastQC	- Trimmomotic	- FastQC	- Bowtie2	- Picard(MarkDuplicates)	- deepTools(multiBamSummary)	- deepTools(plotCorrelation)	- deepTools(plotCoverage)	- MACS2(callpeak)

Launching workflow:

  • Execute Snakefile in snakemake conda env.

Directory structure 

	├── .gitignore	├── README.md	├──Snakefile	├── config	│ ├── config.yaml	│ └── env	│ ├── qc.yaml	│ ├── trim.yaml	│ ├── bowtie2.yaml	│ ├── deeptools.yaml	│ ├── picard.yaml	│ └── macs2.yaml	├── data	│ └── mydatalocal	│ ├── bowtie2	│ └── atacseq	│ └──subset	└── results

  • Datasets go into data/mydatalocal/atacseq/subset

  • Bowtie2 indexes go into data/mydatalocal/bowtie2

  • All output will be in results

  • Snakemake config is in config

  • Conda environment config files are in config/env

Code Snippets

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shell:
    """
    mkdir -p tmp
    gunzip -c {input} > {output}
    """
SnakeMake From line 40 of master/Snakefile 
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shell:
    """
    mkdir -p results/fastqc_init
    fastqc {input} -o "results/fastqc_init" -t {threads}
    """
SnakeMake FastQC From line 54 of master/Snakefile 
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shell:
    """
    mkdir -p results/trim
    trimmomatic PE -threads {threads} \
    -trimlog results/trim/trim.log -summary results/trim/stats \
    {input.r1} {input.r2} \
    {output.fwd_P} \
    {output.fwd_U} \
    {output.rvr_P} \
    {output.rvr_U} ILLUMINACLIP:data/mydatalocal/atacseq/subset/NexteraPE-PE.fa:2:30:10:2:keepBothReads LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:33
    """
SnakeMake Trimmomatic From line 71 of master/Snakefile 
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shell:
    """
    mkdir -p results/fastqc_post
    fastqc {input} -o "results/fastqc_post" -t {threads}
    """
SnakeMake FastQC From line 91 of master/Snakefile 
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shell:
    """
    bowtie2  --very-sensitive -p 1 -k 10  -x data/mydatalocal/bowtie2/all -1 {input.r1}  -2 {input.r2} | samtools view -q 2 -bS  -  |  samtools sort - -o {output.aln}
    samtools index -b {output.aln}
    """
SnakeMake SAMtools Bowtie 2 From line 105 of master/Snakefile 
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shell:
    """
    picard MarkDuplicates \
    I={input.aln_a} \
    O={output.aln_clean} \
    M={output.aln_clean_txt} \
    REMOVE_DUPLICATES=true
    samtools index -b {output.aln_clean}
    """
SnakeMake SAMtools Picard From line 120 of master/Snakefile 
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shell:
    """
    multiBamSummary bins -b {input} \
    -o {output:q}
    """
SnakeMake From line 137 of master/Snakefile 
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shell:
    """
    plotCorrelation \
    -in {input}  \
    --corMethod spearman --skipZeros \
    --plotTitle "Spearman Correlation of Read Counts" \
    --whatToPlot heatmap --colorMap RdYlBu --plotNumbers \
    -o {output.png}   \
    --outFileCorMatrix {output.matrix}
    """
SnakeMake From line 152 of master/Snakefile 
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shell:
    """
    plotCoverage --bamfiles {input} \
    --plotFile {output.png} \
    --plotTitle "Coverage" \
    --outRawCounts {output.matrix} \
    --ignoreDuplicates
    """
SnakeMake From line 172 of master/Snakefile 
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shell:
    """
    macs2 callpeak -t {input}  \
    -f BAM \
    -n {wildcards.sample} \
    --outdir results/macs2
    """
SnakeMake macs2 From line 189 of master/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/mmchaouchi/Cloud
Name: cloud
Version: 1
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