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RNA-seq analysis

Installing TopHat2 on Ubuntu

Dr. Muniba Faiza

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Installing tophat2 on Ubuntu

TopHat is one of the most widely used tools for RNA-seq reads to map splice junction [1]. 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.

Preparing system

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

Installing Pre-requisites

You need to install Bowtie2 before installing TopHat2. Paste the following command in the terminal:

$ sudo apt-get install -y bowtie2

Downloading TopHat2

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

Installing TopHat2

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.


References

  1. 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 biology14(4), 1-13.

Dr. Muniba is a Bioinformatician based in New Delhi, India. She has completed her PhD in Bioinformatics from South China University of Technology, Guangzhou, China. She has cutting edge knowledge of bioinformatics tools, algorithms, and drug designing. When she is not reading she is found enjoying with the family. Know more about Muniba

RNA-seq analysis

RNAdetector- New Tool for RNA-Seq Data Analysis

Tariq Abdullah

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RNAdetector- New Tool for RNA-Seq Data Analysis

In this article, we discuss a new tool that is developed for RNA-Seq data analysis. A new tool called RNAdetector [1] is developed for RNA-Seq data analysis. (more…)

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RNA-seq analysis

RNAIndel: A tool to identify somatic indels from tumor RNA-seq data

Tariq Abdullah

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RNAIndel-predict somatic indels in tumor rna-seq

It is a challenging task to discover somatic coding indels that are generated during the preparation of the PCR-based RNA-seq library. A new tool called RNAIndel [1] has been developed for this purpose. (more…)

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RNA-seq analysis

Differential Gene Expression Analysis of RNA-Seq data using MeV

Dr. Muniba Faiza

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RNA-Seq data analysis

Differential gene expression analysis helps in discovering quantitative changes in the expression levels between the experimental groups. For that, statistical testing is done using various software. In this article, we will analyze RNA seq count data using the edgeR module present in the Multiple Experiment Viewer (MeV) [1,2]. (more…)

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