TopHat

TopHat uses Bowtie, a high-throughput short read aligner, to analyze the mapping results for RNA-Seq reads and identify splice junctions.

 

Please note that tophat (and bowtie) cannot run in parallel, that is, on multiple nodes.  Submitting multi-node jobs will only waste resources.  In addition you must explicitly include the '-p' option to use multiple threads on a single node.

Availability and Restrictions

Versions

TopHat is available on the Owens Cluster. The versions currently available at OSC are:

VERSION OWENS OAKLEY
2.1.1 X* X*
* Current default version

You can use module spider tophat to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.

Access

TopHat is available without restriction to all OSC users.

Publisher/Vendor/Repository and License Type

http://ccb.jhu.edu/software/tophat, Open source

Usage

Usage on Oakley

Set-up

To configure your enviorment for use of TopHat, use command module load tophat. This will load the default version.

Usage on Owens

Set-up

To configure your enviorment for use of TopHat, use command module load tophat. This will load the default version.

Further Reading

Supercomputer: 
Fields of Science: