...
10x scRNA-Seq data is typically processed using various Cell Ranger software tools. These (and other) tools have been combined in an nfcore Nextflow workflow called scrnaseq.
NOTE: sometimes your 10x data has already been processed by your sequencing company, using Cell Ranger. In this case you can skip the nfcore/scrnaseq analysis and go straight to the downstream Seurat analysis.
Workflow overview
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.
...
2. Seurat
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’.
...