Difference between revisions of "TopHat 2016"
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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]. | ||
Revision as of 14:49, 15 January 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 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.
