Whole Transcriptome

The whole transcriptome path processes spatial RNA-seq data generated via DBiT-seq, from raw reads through QC and secondary analysis.

How the workflows fit together

flowchart LR
    FASTQ["FASTQ"] --> PRE["RNAQC"]
    FASTQ -.-> BCQ["BarcodeQC"]
    BCQ -. "cleaning / x-talk input" .-> PRE
    PRE --> OPT["optimize WT"]
    IMAGES["Input Images"] --> OPT
    OPT --> PLOTS["ATX WholeTxn Plots"] & FURTHER{"further<br>analysis?"}
    PLOTS -.-> PLOT_ANALYSES["<b>interactive analysis</b><br>module scoring<br>annotation"]
    FURTHER -- No --> DONE["Analysis Complete"]
    FURTHER -- CoPro --> GLUE["ATX Glue"]
    ATAC["Epigenome Workflow outputs"] --> GLUE
    GLUE --> COPRO["ATX CoPro Plots"]
    COPRO -.-> COPRO_ANALYSES["<b>interactive analysis</b><br>module scoring<br>annotation<br>omics comparison<br>track browser"]

    FASTQ:::startend
    IMAGES:::startend
    BCQ:::process
    PRE:::process
    OPT:::process
    PLOTS:::process
    FURTHER:::decision
    GLUE:::process
    COPRO:::process
    DONE:::startend
    PLOT_ANALYSES:::interactive
    COPRO_ANALYSES:::interactive
    ATAC:::startend
    classDef process stroke:#818cf8,fill:#eef2ff
    classDef decision stroke:#fb923c,fill:#fff7ed
    classDef interactive stroke:#4ade80,fill:#f0fdf4,stroke-dasharray: 5 5
    classDef startend stroke:#a78bfa,fill:#f5f3ff

Walking the flow:

1. Preprocess & QC. Raw FASTQ goes through RNAQC — STARsolo alignment, a MultiQC report, and a FastQ-Screen contamination check — producing the per-run gene-expression matrix. As on the epigenomics path, you can optionally run BarcodeQC first to generate the cleaning and cross-talk correction tables that QC then applies.
2. Optimize (secondary analysis). The QC'd reads plus the spatial images feed optimize_wt, which filters and normalizes, selects highly variable genes, optionally integrates with Harmony, clusters via Scanpy or STAGATE, and computes marker genes. Unlike the epigenomics path, there is no separate object-creation step — optimize_wt is the whole-transcriptome secondary analysis.
3. Visualize & branch. Results are explored in ATX WholeTxn Plots (interactive module scoring and annotation). From the further analysis? decision you either finish, or continue to Co-Profiling — ATX Glue combines these transcriptome outputs with epigenome outputs, visualized in ATX CoPro Plots (module scoring, annotation, omics comparison, track browser).

Processing path

Stage	Workflow	Purpose
Preprocessing	RNAQC	STARsolo alignment, QC report, and contamination screening.
Secondary Analysis	optimize_wt	Preprocessing, integration, clustering, and marker genes.
Plots	Transcriptome Plots	Interactive visualization of results.