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Aim
Analyse 10x Genomics* single cell RNA-Seq data.
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It is also an R package, so we will be using RStudio (which you installed earlier) to run the analysis script.
Open RStudio and create a new R script
RStudio is a GUI (graphical user interface) for R. It makes navigating R easier.
Open RStudio (you can type it in the Windows search bar)
Create a new R script: ‘File’ → “New File” → “R script”
Save this script where your samples folders are (‘File’ → ‘Save’). These should be on your H or W drive. Save the script file as ‘scrnaseq.R’
In the following sections you will be copying and running the R code into your scrnaseq.R script.
Set your working directory
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You can manually set your working directory in RStudio by selecting ‘Session' -> 'Set working directory' -> 'Choose directory'. Choose the same directory as you saved your scrnaseq.R script, previous section. This will output the 'setwd(...)’ command with your working directory into the console window (bottom left panel). Copy this command to replace the default one in the code below setwd(...) line in your R script.
Copy and paste the following code into the R script you just created, then run the code (highlight all the code in your R script, then press the run button).
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