preparations

Title: The Cloud and the Shell - Applied Bioinformatics on the Example of Gene Expression Analysis using Unix and freely available Open Source Tools
Author: Alexander Kerner
EMail: training at silico-sciences.com
Seminar Ruprecht-Karls-Universität Heidelberg

Applied Bioinformatics in the Cloud and in the Shell

RNA-Seq Analysis Using Unix and Open Source Tools

[TOC]

Preparations

0. Install VirtualBox.

1. Download Ubuntu Linux Virtual Machine

ftp://public:[email protected]:/vm.zip.

Unzip and copy the VM folder to

C:\Users\[username]\Virtualbox VMs (Windows) or to

~/VirtualBox VMs (Ubuntu).

0. Start the virtual machine and open a terminal.

1. Verify TopHat is installed.

    $ tophat -v
    TopHat v2.1.0
   

2. Verify Samtools is installed.

    $ samtools
    Program: samtools (Tools for alignments in the SAM format)
    Version: 0.1.19-96b5f2294a
   

3. Verify Cufflinks is installed.

    $ cufflinks
    cufflinks v2.2.1
    linked against Boost version 104700
   

4. Verify RStudio is installed.

   0. Verify cummeRbund is installed.

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