Scanpy FAQ
Common questions about Scanpy input format, GPU acceleration, batch effects, and clustering.
These answers cover the practical choices in Scanpy single-cell analysis on the platform — the required input format, how GPU acceleration works, which workflow to pick, handling batch effects, and how many clusters to expect. For error-by-error fixes, see troubleshooting.
Data preparation
Q: What file format do I need?
A: An AnnData .h5ad file referenced by an S3 URI or HTTPS URL. That's the only format the platform's Scanpy job reads — convert 10X output or CSV matrices to .h5ad first.
Q: Does the .h5ad need to be pre-normalized?
A: No — the pipeline runs QC, normalization, and log-transformation itself. Provide raw counts in X and let the workflow handle preprocessing.
GPU acceleration
Q: Is this GPU-accelerated?
A: Yes. The core workflows (full, qc, clustering, de) run on a T4 GPU via rapids-singlecell (cuML/cuGraph/cupy), which accelerates PCA, k-NN, UMAP, and Leiden. The extension workflows (batch correction, annotation, scoring) run on CPU.
Q: How large a dataset can it handle? A: The T4's 16 GB VRAM is sufficient for up to roughly a million cells. Beyond that, subsample first or filter more aggressively.
Workflows and batch effects
Q: Which workflow should I run?
A: full for the complete pipeline through markers, clustering to stop before differential expression, qc for filtering only, and de for marker genes. Start with full.
Q: How do I handle batch effects?
A: Use one of the batch-correction extension workflows — harmony_integrate, scanorama_integrate, or combat_correct — with a batch_key naming the obs column that holds batch labels. For deep generative integration, pair with scvi-tools.
Clustering
Q: How many clusters should I expect?
A: It depends on your biology. Start at the default resolution of 0.5 and adjust — raise it for more, smaller clusters. Over-clustering is easier to merge than under-clustering is to split.
Q: Leiden or Louvain? A: Leiden (the default) produces better-connected communities and is recommended. Use Louvain only for backward compatibility.
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