Difference between revisions of "TopHat 2016"

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== Installed version ==
== Installed version ==


The currently installed version is available on the environment ''hpc-env/6.4'':
The currently installed version is available on both environments ''hpc-env/6.4'' and ''hpc-uniol-env'':
   TopHat/'''2.1.1-intel-2018a'''
   TopHat/'''2.1.1-intel-2018a'''


== Using TopHat ==
== Using TopHat ==
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Always remember: this command is case sensitive!
Always remember: this command is case sensitive!


You might consider using [[HISAT2 2016 | HISAT2]] instead of TopHat, because HISAT2 provides the same core functionalities as TopHat, but it is considered more effective and accurate.  
''You might consider using [[HISAT2 2016 | HISAT2]] instead of TopHat, because HISAT2 provides the same core functionalities as TopHat, but it is considered more effective and accurate.''


== Documentation ==
== Documentation ==


The full documentation can be found [https://ccb.jhu.edu/software/tophat/manual.shtml here].
The full documentation can be found [https://ccb.jhu.edu/software/tophat/manual.shtml here].

Latest revision as of 13:31, 28 June 2019

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 both environments hpc-env/6.4 and hpc-uniol-env:

 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.