--- license: mit pretty_name: OTTER reproducibility data --- # OTTER reproducibility data This public dataset contains versioned, real-data fixtures and provenance records used to reproduce the executable validation claims for **OTTER** (Orchestrated Transcriptomic, Tumor-xenograft, and Epigenomic Reporting Workflow). ## Scope The dataset contains compact, deterministic derivatives of accessioned sequencing data; BAM/BAI fixtures; expected outputs; Gate A–D oracles; RNA-PDX and BS-PDX mixture inputs; and Xenofilx parameter-grid inputs. It does not contain manuscript materials, private Slurm controllers, full-scale production runs, or full reference-genome snapshots. GitHub Actions consume this dataset for fixture-based checks only. They do not run full FASTQ mapping/alignment. Normal CI reference acquisition uses official upstream FASTA/GTF sources and pinned reference contracts. The separate [`fallingstar10/xdxtools-genomes`](https://huggingface.co/datasets/fallingstar10/xdxtools-genomes) dataset is the offline reference snapshot and is updated only after CI validation. ## Layout ```text provenance/ schema.json files.jsonl checksums.sha256 fastqcx/rna-pdx-srr30880970/ bamdriver/gate-a/rna-pdx-srr30880970/ pairbam/gate-b/rna-pdx-srr30880970/ xenofilx/gate-c/{rna-hg38,bs-pdx-graft-hg38,bs-pdx-srr36187610-host}/ xenofilx/gate-d/bs-pdx-srr36187610/ xenofilx/mixture/rna-pdx//{graft.bam,host.bam,truth.tsv} xenofilx/mixture/bs-pdx//{graft.hg19.bam,host.mm10.bam,truth.tsv} xenofilx/benchmark/tables/{note4-summary-table.csv,note4-confusion-matrix-table.csv,table-s5-gradient.tsv,table-s6-gradient.tsv,table-s7-parameter-grid.tsv} ``` Each line in `provenance/files.jsonl` conforms to `provenance/schema.json`. The required `owner` object identifies the repository, workflow, validation gate, and assay. The required `derivation` object records the SRA accession, Paracloud source path, method, seed when applicable, and input/output counts. ## Mixture gradients (Supplementary Note 4) `xenofilx/mixture/bs-pdx/` holds the complete 0–99% bisulfite composition gradient behind Supplementary Table S6: 43 cells, each with a human-graft alignment to bisulfite-converted hg19, a mouse-host alignment to bisulfite-converted mm10, and a per-fragment construction truth. Cell labels are `human0-replicate1` (pure-mouse control) and `human0p-replicate`, for example `human0p5-replicate1` (50% human). Sources are human RRBS `SRR31480456` and mouse RRBS `SRR10025242`, aligned with Bismark 3.1.0; each cell carries 1,000,000 complete fragments. The three replicates of the 60% cell (`human0p6-replicate1..3`) are also the inputs of the Supplementary Table S7 threshold/penalty audit. Every file's SHA-256 matches the value recorded by the original evaluation manifests, so the published fixtures are provably the same bytes those analyses consumed. `xenofilx/mixture/rna-pdx/` holds the complete 0–99% RNA-seq composition gradient behind Supplementary Table S5: 43 cells, each with a human-graft alignment to hg38 (STAR), a mouse-host alignment to mm10 (STAR), and a per-fragment construction truth. Cell labels are `human0-replicate1` (pure-mouse control) and `human0p-replicate`, for example `human0p5-replicate1` (50% human). Sources are human RNA-seq `SRR1039508` and mouse RNA-seq `SRR037954`, aligned with STAR; each cell carries 1,000,000 complete fragments (n=3 replicates per non-zero fraction). Every file's SHA-256 matches the value recorded by the evaluation manifests. ## Benchmark tables and confusion matrices (Supplementary Note 4) `xenofilx/benchmark/tables/` publishes the machine-readable summary tables, confusion matrices, and audit manifests corresponding to Supplementary Tables S5, S6, and S7: - `note4-summary-table.csv` — Unified 117-row x 24-column cross-assay benchmark summary covering the RNA-seq 0–99% gradient (n=3), BS-seq 0–99% gradient (n=3, three arms), BS-seq 60% parameter grid (n=3, three arms), and authentic PDX accessions (`SRR30880970`, `SRR36187610`). - `note4-confusion-matrix-table.csv` — Comprehensive 446-row x 32-column table recording the full 2x2 confusion matrix (TP, FN, FP, TN exact integer counts and derived rates) for every single replicate (329 rows) and stratum mean (117 rows). - `table-s5-gradient.tsv` — RNA-seq 0–99% gradient benchmark table (14 non-zero points n=3). - `table-s6-gradient.tsv` — BS-seq 0–99% gradient benchmark table with modern, patched legacy, and conventional unpatched paths (all n=3). - `table-s7-parameter-grid.tsv` — 4x3 mismatch threshold and unmapped penalty factorial grid across all three paths (n=3). - `table-s8-reference-grid.tsv` — 2x2 factorial reference genome combination benchmark (hg19/hg38 x mm10/mm39) on 60% BS-seq mixtures across all three tool paths (n=3). - `note4-reference-grid-summary.csv` — Reference genome combination summary table (12 stratum mean rows). - `note4-reference-grid-confusion-matrix.csv` — Complete 48-row x 28-column table recording the full 2x2 confusion matrix (TP, FN, FP, TN integer counts and derived rates) for all 36 individual evaluations and 12 stratum means. - `per-cell-expected-s5.json`, `per-cell-expected-s6.json`, `per-cell-expected-s7.json` — Machine-auditable per-cell reference metric targets used by CI parity gates. - `rna-mixture-cells.json` — Immutable fixture contract for all 43 RNA-PDX mixture cells. ## Validation policy - All supplied files are checksum-verified before use. - RNA-PDX and BS-PDX evidence is independently scoped. - Xenofilx parameter recommendations apply only to the documented assay and fixture. - Results and logs from scientific CI are published as GitHub Actions artifacts, including failure cases. - Full raw-read mapping, manuscript-scale benchmarking, and private Paracloud operations are outside GitHub-hosted CI. ## Citation Use the future OTTER software release tag together with the exact Hugging Face dataset revision SHA shown by the workflow or provenance record.