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Analyse 10x Genomics* single cell RNA-Seq data.
This analysis workflow is split into 2 main sections: 1) ‘Upstream’ analysis on QUT’s HPC (high performance compute cluster) using aNextflow workflow, nfcore/scrnaseq, 2) ‘Downstream’ analysis in R, primarily using the package seurat.
*Note: this workflow can be adapted to work with scRNA-Seq datasets generated by other sequencing technologies than 10x Genomics.
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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