Single-cell RNA-seq pipeline, release p1.1
phalaena:pipeline:PA-PL-transcriptomics-cellseq
Single-cell RNA-seq on 10x Chromium 3' data. We parse 10x-style FASTQs (both the pre-paired v2/v3 layout and the v1 RA-interleaved chunk layout), align with STARsolo in a single pass that does alignment, barcode demultiplexing, and UMI collapsing together, detect doublets with Scrublet, run a baseline Scanpy analysis (filtering, normalization, highly-variable-gene selection, PCA, k-NN graph, UMAP, Leiden clustering), and emit a canonical summary/summary.json matching phalaena_backend/pipelines/SUMMARY_SCHEMA.md. The assistant reads this contract directly. Pipeline ID transcriptomics_cellseq. Source: phalaena_backend/pipelines/2.2_transcriptomics_cellseq/. API entry: phalaena_api/app/pipelines/transcriptomics_cellseq.py.
- kind
- pipeline
- status
- reviewed
- github:phalaena-automata/monorepo/phalaena_backend/pipelines/2.2_transcriptomics_cellseq
View Single-cell RNA-seq pipeline, release p1.1 on the Phalaena Wiki