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As can be seen in the workflow below, there are several workflow options. The one we’ll be using is the complete Cell Ranger workflow, using the tools cellranger mkgtf and cellranger mkref for reference genome preparation and cellranger count for both aligning sequences to the reference genome and quantifying expression per gene per cell, for each sample.

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2. Seurat

Seurat is:

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.

Cell Ranger (and nfcore/scrnaseq) generates a default directory and file output structure for each sample, which we’ll use in R to complete our analysis. Each sample will have a directory named after the sample, an ‘outs’ subdirectory under this. This ‘outs’ directory contains various files and subdirectories. The subdirectory that contains the count matrix data we need for Seurat analysis is called ‘filtered_feature_bc_matrix’.

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