Outputs_structure.md

April 10, 2024 · View on GitHub

Introduction: Quick Start, Tutorial, Flowchart, Outputs structure
Install: Dependencies, Containers, References, Test datasets
Inputs: Data, Design, Parameters
1. Preprocessing: ATAC reads, ATAC peaks, mRNA
2. Differential Analysis: ATAC, mRNA, Split
3. Enrichment Analysis: Enrichment, Figures, Tables

.
├── Figures_Individual
│   ├── 1_Preprocessing
│   │   ├── ATAC__peaks__average_profile
│   │   ├── ATAC__peaks__coverage
│   │   ├── ATAC__peaks__grouped_plots
│   │   ├── ATAC__peaks__saturation_curve
│   │   ├── ATAC__reads__correlations
│   │   ├── ATAC__reads__coverage
│   │   ├── ATAC__reads__insert_size
│   │   └── ATAC__reads__PCA
│   ├── 2_Differential_Analysis
│   │   ├── ATAC__FDR_by_PA
│   │   ├── ATAC__other_plots
│   │   ├── ATAC__PCA_1_2
│   │   ├── ATAC__PCA_3_4
│   │   ├── ATAC__volcano
│   │   ├── mRNA__other_plots
│   │   ├── mRNA__PCA_1_2
│   │   ├── mRNA__PCA_3_4
│   │   ├── mRNA__volcano
│   │   ├── Venn_diagrams__four_ways
│   │   └── Venn_diagrams__two_ways
│   └── 3_Enrichment_Analysis
│       ├── Barplots__CHIP
│       ├── Barplots__chrom_states
│       ├── Barplots__func_anno_BP
│       ├── Barplots__func_anno_KEGG
│       ├── Barplots__genes_self
│       ├── Barplots__motifs
│       ├── Barplots__peaks_self
│       ├── Heatmaps__CHIP
│       ├── Heatmaps__chrom_states
│       ├── Heatmaps__func_anno_BP
│       ├── Heatmaps__func_anno_KEGG
│       ├── Heatmaps__genes_self
│       ├── Heatmaps__motifs
│       └── Heatmaps__peaks_self
├── Figures_Merged
│   ├── 1_Preprocessing
│   ├── 2_Differential_Analysis
│   └── 3_Enrichment_Analysis
├── Processed_Data
│   ├── 1_Preprocessing
│   │   ├── ATAC__peaks__annotated_rds
│   │   ├── ATAC__peaks__split__no_BL_input_RNAi
│   │   ├── ATAC__reads__bam
│   │   ├── ATAC__reads__bam_no_lowQ
│   │   ├── ATAC__reads__bam_no_lowQ_dupli
│   │   ├── ATAC__reads__bam_no_lowQ_dupli_mito
│   │   ├── ATAC__reads__fastq_trimmed
│   │   ├── mRNA__fastqc
│   │   └── mRNA__kallisto_output
│   ├── 2_Differential_Analysis
│   │   ├── ATAC__all_peaks__bed
│   │   ├── ATAC__all_peaks__ChIPseeker
│   │   ├── ATAC__all_peaks__dataframe
│   │   ├── ATAC__all_peaks__DiffBind
│   │   ├── ATAC__all_peaks__gRange
│   │   ├── ATAC__non_annotated_peaks
│   │   ├── DA_split__bed_regions
│   │   ├── DA_split__genes_rds
│   │   ├── mRNA__all_genes__bed_promoters
│   │   └── mRNA__all_genes__rsleuth
│   └── 3_Enrichment_Analysis
│       ├── Barplots__CHIP
│       ├── Barplots__chrom_states
│       ├── Barplots__func_anno_BP
│       ├── Barplots__func_anno_KEGG
│       ├── Barplots__genes_self
│       ├── Barplots__motifs
│       ├── Barplots__peaks_self
│       ├── Enrichment__CHIP
│       ├── Enrichment__chrom_states
│       ├── Enrichment__func_anno_BP
│       ├── Enrichment__func_anno_KEGG
│       ├── Enrichment__genes_self
│       ├── Enrichment__motifs
│       ├── Enrichment__motifs__raw
│       ├── Enrichment__peaks_self
│       ├── Heatmaps__CHIP
│       ├── Heatmaps__chrom_states
│       ├── Heatmaps__func_anno_BP
│       ├── Heatmaps__func_anno_KEGG
│       ├── Heatmaps__genes_self
│       ├── Heatmaps__motifs
│       └── Heatmaps__peaks_self
├── Tables_Individual
│   ├── 1_Preprocessing
│   ├── 2_Differential_Analysis
│   │   ├── ATAC_detailed
│   │   ├── mRNA_detailed
│   │   ├── res_filter
│   │   └── res_simple
│   └── 3_Enrichment_Analysis
│       ├── CHIP
│       ├── chrom_states
│       ├── func_anno_BP
│       ├── func_anno_KEGG
│       ├── genes_self
│       ├── motifs
│       └── peaks_self
└── Tables_Merged
    ├── 1_Preprocessing
    ├── 2_Differential_Analysis
    └── 3_Enrichment_Analysis

Cactus produces three main types of outputs: processed data, figures and tables. Both figures and tables are available as merged files (for easier scrolling) or as individual files (for lower memory usage). Tables can be either csv files or formatted Excel files.