TopHat is one of the most widely used tools for RNA-seq reads to map splice junction . It uses Bowtie to align mammalian genomes. The older versions of TopHat require the separate installation of SAMTools. But the versions 2.0 onwards come with an inbuilt stable SAMTools package. In this article, we will install TopHat2.1.1. on Ubuntu.
Open a terminal by pressing Ctrl+Alt+T. Update and upgrade your system using the following commands:
$ sudo apt-get update
$ sudo apt-get upgrade
You need to install Bowtie2 before installing TopHat2. Paste the following command in the terminal:
$ sudo apt-get install -y bowtie2
Change to the directory where you want to download the software. Let’s say, Downloads. Download the latest release of TopHat2 from here or use the following command:
$ cd Downloads/
$ wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
Extract the downloaded file using the following command:
$ tar xvzf tophat-2.1.1.Linux_x86_64.tar.gz
Change to the source directory of tophat,
$ cd tophat-2.1.1.Linux_x86_64/
Now copy tophat2 and tophat binaries to the path as shown below:
$ sudo cp tophat2 /usr/bin
$ sudo cp tophat /usr/bin
Now you can run tophat2 by typing
$ tophat2in the terminal. It should display the usage.
- Kim, D., Pertea, G., Trapnell, C., Pimentel, H., Kelley, R., & Salzberg, S. L. (2013). TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome biology, 14(4), 1-13.