3  Build 01 · RNA-seq System

End-to-end RNA-seq workflow for reproducible transcriptomics analysis and interpretation.

3.1 System Path

flowchart TD

    A[FASTQ Files]
    B[FastQC]
    C[Trimming if Needed]
    D[Quantification or Alignment]
    E[MultiQC Aggregation]
    F[Count Matrix]
    G[DESeq2]
    H[Exploration]
    I[Differential Expression]
    J[Interpretation]
    K[Quarto Reporting]

    A --> B
    B --> C
    C --> D
    D --> E
    E --> F
    F --> G
    G --> H
    H --> I
    I --> J
    J --> K

    style A fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#0f172a
    style B fill:#e0f2fe,stroke:#0284c7,stroke-width:2px,color:#0f172a
    style C fill:#ecfeff,stroke:#0891b2,stroke-width:2px,color:#0f172a
    style D fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#0f172a
    style E fill:#f3e8ff,stroke:#9333ea,stroke-width:2px,color:#0f172a
    style F fill:#fae8ff,stroke:#c026d3,stroke-width:2px,color:#0f172a
    style G fill:#fef3c7,stroke:#d97706,stroke-width:2px,color:#0f172a
    style H fill:#fde68a,stroke:#ca8a04,stroke-width:2px,color:#0f172a
    style I fill:#ecfccb,stroke:#65a30d,stroke-width:2px,color:#0f172a
    style J fill:#d1fae5,stroke:#059669,stroke-width:2px,color:#0f172a
    style K fill:#f0fdf4,stroke:#16a34a,stroke-width:2px,color:#0f172a

flowchart TD

    A[FASTQ Files]
    B[FastQC]
    C[Trimming if Needed]
    D[Quantification or Alignment]
    E[MultiQC Aggregation]
    F[Count Matrix]
    G[DESeq2]
    H[Exploration]
    I[Differential Expression]
    J[Interpretation]
    K[Quarto Reporting]

    A --> B
    B --> C
    C --> D
    D --> E
    E --> F
    F --> G
    G --> H
    H --> I
    I --> J
    J --> K

    style A fill:#dbeafe,stroke:#2563eb,stroke-width:2px,color:#0f172a
    style B fill:#e0f2fe,stroke:#0284c7,stroke-width:2px,color:#0f172a
    style C fill:#ecfeff,stroke:#0891b2,stroke-width:2px,color:#0f172a
    style D fill:#ede9fe,stroke:#7c3aed,stroke-width:2px,color:#0f172a
    style E fill:#f3e8ff,stroke:#9333ea,stroke-width:2px,color:#0f172a
    style F fill:#fae8ff,stroke:#c026d3,stroke-width:2px,color:#0f172a
    style G fill:#fef3c7,stroke:#d97706,stroke-width:2px,color:#0f172a
    style H fill:#fde68a,stroke:#ca8a04,stroke-width:2px,color:#0f172a
    style I fill:#ecfccb,stroke:#65a30d,stroke-width:2px,color:#0f172a
    style J fill:#d1fae5,stroke:#059669,stroke-width:2px,color:#0f172a
    style K fill:#f0fdf4,stroke:#16a34a,stroke-width:2px,color:#0f172a

3.2 Core Tools

• FastQC
• MultiQC
• Salmon
• STAR
• featureCounts
• DESeq2
• Quarto

3.3 Status

Active flagship build.

3.4 Live Build

rnaseq.complexdatainsights.com