Reference: Computational Pipelines Doc
| Step | v1 | v2 | v3 |
|---|---|---|---|
| Preprocessing | CellRanger | CellRanger | Single cell uniform pipeline |
| Sample QC | Multiome Sample QC Pipeline | Multiome Sample QC Pipeline | Multiome Sample QC Pipeline |
| Cell annotation | Multiome Cell Annotation Pipeline | Multiome Cell Annotation Pipeline | Multiome Cell Annotation Pipeline |
| Peak calling | SnapATAC2 + MACS3 | SnapATAC2 + MACS3 (refined) | — |
| Differential analysis | DESeq2 pseudobulk | DESeq2 pseudobulk (refined) | — |
| Peak-to-gene linking | — | — | — |
| Sequence modeling | ChromBPNet | — | — |
Code in igvf-data/igvf_sc-islet_10X-Multiome/scratch/2026_01_30/ and scratch/2026_02_02/.
| Step | Description |
|---|---|
| 1. RNA QC | Filter low-quality RNA barcodes (1_qc_RNA.tsv) |
| 2. ATAC QC | AMULET doublet detection + ATAC filtering (2_AMULET.tsv, 2_integrate_ATAC.tsv) |
| 3. Sample QC | Per-sample QC, normalization, and initial clustering (RNA + ATAC) |
| 4. Integration | Cross-sample Harmony integration, cell type annotation |
| 5. Peak calling | SnapATAC2 MACS3 peak calling, annotation, pseudobulk peak matrices |
| 6. Joint analysis | Joint RNA-ATAC embedding, gene activity quantification, multiome correlation |
| 7. Differential analysis | DESeq2 pseudobulk DE (RNA) and DA (ATAC), DEGPatterns, complex heatmaps |
| 8. ChromBPNet | Sequence model training, contribution scores, TF-MoDISco motifs, variant scoring |
| 9. Upload | Cell-by-X matrices, pseudobulks, browser tracks, GRN outputs |
Code in igvf-data/igvf_sc-islet_10X-Multiome/bin/.
| Step | Description |
|---|---|
| 1. Get data | Transfer FASTQs from TSCC, download portal metadata |
| 2. Process data | CellRanger-ARC count, run QC on CellRanger outputs |
| 3. Sample QC | RNA QC filtering, AMULET doublet detection, ATAC QC filtering |
| 4. Integration | Merge + Harmony integration (RNA, ATAC), cell annotation, pseudobulk generation |
| 5. Peak calling | MACS3 peak calls per celltype-condition, consensus peaks, peak matrices |
| 6. Differential analysis | DESeq2 pseudobulk RNA, DEG summaries, DEGPatterns |
| 9. Upload | Upload to gs://igvf-data/ via notebook |
| 10. Submission | MD5sums, IGVF portal metadata tables, seqspec, analysis sets |
- 2025_01_13 — DEG Updates
- 2025_03_25 — Collinearity Issues
- 2026_02_19 — IGVF BCN Agenda (differential analysis)
Pipeline details coming soon