TopHat 2016

Introduction

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes, and then analyzes the mapping results to identify splice junctions between exons.¹

Installed version

The currently installed version is available on the environment hpc-env/6.4:

 TopHat/2.1.1-intel-2018a

Using TopHat

If you want to find out more about TopHat on the HPC Cluster, you can use the command

module spider TopHat

This will show you basic informations e.g. a short description and the currently installed version.

To load the desired version of the module, use the command, e.g.

module load hpc-env/6.4
module load TopHat

Always remember: this command is case sensitive!

You might consider using HISAT2 instead of TopHat, because HISAT2 provides the same core functionalities as TopHat, but it is considered more effective and accurate.

Documentation

The full documentation can be found here.