Aim
Analyse 10x Genomics* single cell RNA-Seq data.
*Note: this workflow can be adapted to work with scRNA-Seq datasets generated by other sequencing technologies than 10x Genomics.
Requirements
A HPC account. If you do not have one, please request one here.
Access to an rVDI virtual desktop machine with 64GB RAM. For information about rVDI and requesting a virtual machine, see here.
Nextflow installed on your HPC home account. If you haven’t already installed Nextflow, do so by following the guide here.
Your scRNA-Seq data (fastq files) are on the HPC. If you are having difficulties transferring them to the HPC, submit a support ticket here.
Connect to an rVDI virtual desktop machine
scRNA-Seq datasets are often very large, requiring a lot of memory to run. Downstream analysis is run in R, on a Windows machine. Your PC is unlikely to have enough RAM, thus we’re using virtual machines with 64GB RAM. In addition, you can run the rest of this analysis in the virtual machine.
To access and run an rVDI virtual desktop:
Go to https://rvdi.qut.edu.au/
Click on ‘VMware Horizon HTML Access’
Log on with your QUT username and password
*NOTE: you need to be connected to the QUT network first, either being on campus or connecting remotely via VPN.