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Cell Ranger .h5, a zipped matrix folder, .h5ad, or FASTQ. Up to 500 GB per file.

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Species

Clustering detail Higher gives more, smaller clusters. 0.8 suits most data.

Quality filters

Minimum genes per cell Fewer usually means an empty droplet.

Maximum % mitochondrial More usually means a damaged cell.

Maximum genes per cell 0 means no limit.

Remove likely doublets