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*NOTE: you need to be connected to the QUT network first, either being on campus or connecting remotely via VPN.
1. nfcore/scrnaseq
Upstream analysis 10x scRNA-Seq data is typically processed using Cell Ranger
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.
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’.