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Getting the prerequiesites

Creating a folder​

To start this practical we suggest working the following way:

  1. Create a new folder on your Desktop - called 'genomics_tutorial' for example.

  2. Start an RStudio session and make sure you have this set as your working directory as follows:

  • from the top menu bar, select 'Session'
  • select 'Set Working Directory'
  • 'Choose Directory'
  • navigate through your file system to the new directory folder
  • click 'Open'
  1. Also open your Ubuntu for Windows terminal and change directory:
cd /mnt/c/Users/(your username)/Desktop/genomics_tutorial
Note

You will have to put your username (gmXX) in there. Remember you can use tab completion to quickly complete paths like this.

Installing R libraries​

In this tutorial we will use several R packages to work with genomic data. You will need to install these on your system first. Let's start by installing these now:

if (!require("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::install("rtracklayer")
BiocManager::install("GenomicRanges")
BiocManager::install("Gviz")
BiocManager::install("VariantAnnotation")
BiocManager::install("GenomicFeatures")

When it's time to use these, we will load them into our R session using the library() command, e.g.:

library( rtracklayer )

(The tutorial will tell you when to do this.)

When you've installed the packages, get started with the tutorial.