Single-cell RNA-seq

Use this skill for scRNA-seq or snRNA-seq kickoff from FASTQs, Cell Ranger-style outputs, matrices, .h5, .h5ad, or .rds. This skill owns upstream intake and FASTQ-to-count routing; post-count QC, annotation, clustering, and UMAPs must route to the embedded scrna-seq-qc skill.

Essential Inputs

Confirm:

• input type: FASTQ, count matrix, .h5, .h5ad, or .rds
• assay: single-cell or single-nucleus
• chemistry or barcode/UMI layout
• organism and reference
• expected cells per sample when available
• sample, donor, batch, and channel metadata
• desired endpoint: count matrix only, QC, clustering, annotation, UMAP, or differential abundance/expression

Public Default

For FASTQs, prefer public alternatives: