Workflow Steps and Code Snippets

150 tagged steps and code snippets that match keyword DeepTools

Snakemake-based workflow for the assembly of chloroplast genomes

shell:
    """
    bamCoverage -b {input} -o {output.bigwig}
    """

SnakeMake DeepTools From line 166 of main/Snakefile

shell:
    """
    bamCoverage -b {input} -o {output.bigwig}
    """

SnakeMake DeepTools From line 271 of main/Snakefile

In this repository, we present the code for the analysis of study of the transcription's impact on Escherichia coli chromosome.

shell:
    """
    samtools sort {input.bam} -@ {threads} -o {params.sorted_bam}
    samtools index {params.sorted_bam} -@ {threads}
    bamCoverage --bam {params.sorted_bam} \
        --outFileName {output.unstranded} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM 
    """

SnakeMake SAMtools DeepTools From line 53 of rules/01_hic_processing.smk

shell:
    """
    samtools index {input.bam} -@ {threads}
    bamCoverage --bam {input.bam} \
        --outFileName {output.unstranded} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM \
        --extendReads 200
    bamCoverage --bam {input.bam} \
        --outFileName {output.fw} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM \
        --extendReads 200 \
        --filterRNAstrand forward
    bamCoverage --bam {input.bam} \
        --outFileName {output.rv} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM \
        --extendReads 200 \
        --filterRNAstrand reverse
    """

SnakeMake SAMtools DeepTools From line 86 of rules/02_rna_processing.smk

shell:
    """
    samtools index {input} -@ {threads}
    bamCoverage --bam {input} \
        --outFileName {output.unstranded} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM \
        --extendReads 200
    bamCoverage --bam {input} \
        --outFileName {output.fw} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM \
        --extendReads 200 \
        --filterRNAstrand forward
    bamCoverage --bam {input} \
        --outFileName {output.rv} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM \
        --extendReads 200 \
        --filterRNAstrand reverse
    """

SnakeMake SAMtools DeepTools From line 142 of rules/02_rna_processing.smk

shell:
    """
    samtools index {input.bam} -@ {threads}
    bamCoverage --bam {input.bam} \
        --outFileName {output.unstranded} \
        --binSize 1 \
        --numberOfProcessors {threads} \
        --normalizeUsing CPM \
        --extendReads 
    """

SnakeMake SAMtools DeepTools From line 57 of rules/03_chip_processing.smk

Small snakemake pipeline to explore RNA-Seq data with deepTools. (v2.0.0)

shell:
    """
    bamCoverage \
    --bam {input.BAM_sorted} \
    --outFileName {output.BW_sample} \
    --binSize 1 \
    --outFileFormat bigwig \
    --numberOfProcessors {resources.threads} \
    2> {log.LOG_local_log};
    """

SnakeMake DeepTools From line 186 of master/Snakefile

Snakemake Workflow for ATAC-seq Data Re-analysis on a Compute Cluster

shell:
    """
    mkdir -p results/deeptools
    multiBamSummary bins --bamfiles {input} -o {output}
    """

SnakeMake DeepTools From line 167 of main/Snakefile

shell:
    """
    plotCorrelation -in {input.npz} -p heatmap -c pearson -o {output.heatmap} --removeOutliers
    bamCoverage -b {input.bam} -o {output.bedgraph} -of bedgraph
    bamPEFragmentSize -b {input.all} --samplesLabel 0h_R1 0h_R2 0h_R3 24h_R1 24h_R2 24h_R3 --table {output.tsv} -o {output.hist}
    """

SnakeMake DeepTools From line 190 of main/Snakefile

shell:
    """
    mkdir -p results/deeptools
    cat {input.zero} > {output.Peakzero}
    cat {input.vingtquatre} > {output.Peakvingtquatre}
    sort -k1,1 -k2,2n {output.Peakzero} | bedtools merge -i - > {output.bedzero}
    sort -k1,1 -k2,2n {output.Peakvingtquatre} | bedtools merge -i - > {output.bedvingtquatre}
    bedtools intersect -wa -a {input.zero} -b {input.vingtquatre} > {output.common}
    bedtools intersect -wa -v -a {input.zero} -b {input.vingtquatre} > {output.uniquezero}
    bedtools intersect -wa -v -a {input.vingtquatre} -b {input.zero} > {output.uniquevingtquatre}
    """