Chunk #14 — Methods — Alignment and initial processing of single cell sequencing data

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Multiplexed droplet single-cell RNA-sequencing using natural genetic variation.

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yes

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We used the CellRanger v1.1 and v1.2 software with the default settings to process the raw FASTQ files, align the sequencing reads to the hg19 transcriptome, and generate a filtered UMI expression profile for each cell17. The raw UMI counts from all cells and genes with nonzero counts across the population of cells were used to generate t-SNE profiles.