ATAC-Seq Data Analysis Pipeline for Identifying Nuclear Sites in Ikaros Translocation Study

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This is a ATACSeq snakemake pipeline for High Performance Computing course. We first did the ATACSeq data analysis with slurm (https://github.com/dijashis/Projet_HPC) . We use ATAC-Seq data from Gomez-Cabrero et al. (2019) from a murine B3 cell line. One of the goals of the study is to identify new nuclear sites following translocation of the transcription factor Ikaros after exposure to the drug Tamoxifen The original data set has 50,000 cells collected per sample 3 replicates per sample and 2 cell stages: 0 and 24h (harvest time after drug treatment). Use (https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html) for reproducibility.

To launch the pipeline you we need :

Files that should be in data/mydatalocal/atacseq/ ( subsets and bowtie2 index)
One config files detailling all the different options and data needed to launch the pipe. config/config.yaml in the config directory
Snakefiles (entrypoint of the workflow contains rules and scripts)
env.yaml ( we need conda with bioconda and conda-forge and the following dependancies for all rules in snakefile )

dependencies :

- FastQC==0.11.9
- Cutadapt==3.5 
- Bowtie2 
- samtools==1.14
- r-base==4.1.1
- openjdk==10.0.2
- picard==2.26.5
- deepTools 
- MACS2
- bedtools

Code Snippets

shell:
    """
    mkdir -p tmp
    gunzip -c {input} > {output}
    """

SnakeMake From line 39 of main/Snakefile

shell:
    """
    mkdir -p results/fastqc_init
    fastqc {input} -o "results/fastqc_init" -t {threads}
    """

SnakeMake FastQC From line 54 of main/Snakefile

shell:
    """
    mkdir -p results/trimming
    cutadapt -j {threads} -a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA -o {output.clean_R1} -p {output.clean_R2} {input.read} {input.read2}
    """

SnakeMake Cutadapt From line 72 of main/Snakefile

shell:
    """
    mkdir -p results/fastqc_post_trim
    fastqc {input} -o "results/fastqc_post_trim" -t {threads}
    """

SnakeMake FastQC From line 87 of main/Snakefile

shell:
    """
    mkdir -p results/bowtie2
    bowtie2  --very-sensitive -p {threads} -x data/mydatalocal/atacseq/bowtie2/all -1 {input.R1} -2 {input.R2} |  samtools view -q 2 -bS  -  |  samtools sort - -o {output.bam}
    """

SnakeMake SAMtools Bowtie 2 From line 103 of main/Snakefile

shell:
    """
    mkdir -p results/picard
    picard MarkDuplicates -I {input.map} -O {output.bamnet} -M {output.net_txt} -REMOVE_DUPLICATES true
    samtools index -b {output.bamnet}
    """

SnakeMake SAMtools Picard From line 119 of main/Snakefile

shell:
    """
    mkdir -p results/deeptools
    plotCoverage --bamfiles {params.bam} --plotFile {output.plot_cov} --smartLabels --plotFileFormat pdf -p 6
    multiBamSummary bins --bamfiles {params.bam} -o {output.summary} -p 6
    plotCorrelation -in {output.summary} --corMethod spearman --skipZeros --whatToPlot heatmap --colorMap RdYlBu --plotNumbers -o {output.plot_corr}
    """

SnakeMake DeepTools From line 136 of main/Snakefile

shell:
    """
    mkdir -p results/macs
    macs2 callpeak -t {input.pic} -f BAM -n {params.nom} --outdir {params.rep}
    """

SnakeMake macs2 From line 159 of main/Snakefile

shell:
    """
    mkdir -p results/bedtools
    bedtools intersect -a {input.zero} -b {input.V} > {output.commun}
    bedtools intersect -v -a {input.zero} -b {input.V} > {output.uniquezero}
    bedtools intersect -v -a {input.V} -b {input.zero} > {output.onlyV}
    """