How can I setup Geneious to analyse RNA-Seq using DESeq2, on Linux?

The option to analyze RNA-Seq data using DESeq2 within Geneious is available in R10.1 and later.  To do this on a Linux computer, you will first need to install R and the DESeq2 package, following the instructions below.  This is only necessary for Linux systems, as Geneious will automatically install R on Windows and MacOS systems the first time DESeq2 is run. 

Once R has been installed, you will be able to run the DESeq2 method to Compare Expression Levels within Geneious like any other Geneious operation. You may need to specify the R executable location in the DESeq2 options, for example, if R is not installed on PATH.

Note that the installation instructions for R on Ubuntu, Centos or Red Hat Enterprise Linux require sudo or root access. If you do not have root access, you can install R from source in your home directory.

Installing R

Install R version 3.3.0 or greater.  For more information, or more detailed instructions for select Linux distributions, refer to the R Project website.

R installation on Ubuntu:

  1. On the terminal, enter the following commands to install R and its dependencies:

            $ sudo apt-get install libcurl4-openssl-dev libxml2-dev
            $ sudo apt-get install r-base r-base-dev

  2. You can now proceed with DESeq2 installation

R installation on Centos or Red Hat Enterprise Linux:

  1. On the terminal, enter the following commands to install R’s dependencies:

            $ sudo yum install curl
            $ sudo yum install libcurl libcurl-devel
            $ sudo yum install libxml2 libxml2-devel

  2. Now install R with the following command:  

            $ sudo yum install R

  3. You can now proceed with DESeq2 installation

R installation from source in your home directory:

You should only install R from source in your home directory if you do not have root access.

  1. Download the R source archive from the R project website
  2. On the terminal, go to the directory where you downloaded the the source
  3. Extract the archive:

            $ tar -xvzf R-3.X.Y.tar.gz (replace 3.X.Y with the version you are installing)

  4. Enter the source directory:

            $ cd R-3.X.Y

  5. Run the following commands to build and install R:

            $ ./configure --prefix=$HOME/R
            $ ./configure --prefix=$HOME/R

    Note that if the first command fails because of missing libraries, it may still be possible to install these dependencies without root access, but this is beyond the scope of this Knowledge Base entry

This will install R in your home directory under   $HOME/R/bin.

You can add this directory to your PATH variable or run R from the terminal with the command   ~/R/bin/R.

You can now proceed with DESeq2 installation.

Installing DESeq2

Once you have installed R, you must install Bioconductor, then use Bioconductor to install DESeq2. Only DESeq2 version 1.14.1 is currently supported.

  1. From the terminal, launch R normally using the command R
  2. Install Bioconductor:

            > source("https://bioconductor.org/biocLite.R")

  3. Install DESeq2:

          > biocLite("DESeq2")

    Note that you will be asked to install any dependent packages that are not already installed. This step can take some time: wait for it to finish before proceeding
  4. Quit R by entering   CTRL-D.
    You will be asked whether you’d like to save your workspace image; you may answer ‘n’ (answer ‘y’ if you’d like to use R from the terminal in the future and wish to save the history of the commands you used)
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