Pipelines
Complete workflows, maintained in place. Each page lists inputs, software, the full job script, known issues and a changelog. Individual runs are logged in the notebook and link back here.
| Title | Description | Updated |
|---|---|---|
| 10x scRNA-seq: Cell Ranger → GeneExt → CellBender | From FASTQs to ambient-RNA-corrected count matrices for non-model invertebrates, with GeneExt-extended gene models. Runs as an LSF job chain on an HPC cluster. | 2026-10-16 |
| Coral proteome functional annotation | Annotate every gene model in a coral proteome with orthologs, domains, signal peptides, transmembrane topology and a functional class, merged into one master table per species. Eight LSF jobs per species. | 2026-10-16 |
| Multi-species orthology with OrthoFinder | Find orthogroups and pairwise orthologs across several cnidarian proteomes in a single OrthoFinder run, ready for cross-species marker transfer and comparative genomics. One LSF job. | 2026-10-16 |
| scRNA-seq QC and cluster calling (Seurat) | From CellBender-cleaned 10x counts to integrated, clustered Seurat objects: threshold filtering, doublet removal, SCTransform integration, and data-driven choices of PCs, UMAP settings and clustering resolution. Two R Markdown templates. | 2026-10-16 |
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Older central documents
These overview pages from the old notebook are being folded into pipelines: