Tophat

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Revision as of 02:03, 10 August 2012 by Moskalenko (talk | contribs) (Text replace - "==Running the application using modules==" to "==Execution Environment and Modules==")
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Description

tophat website  

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

Tophat is a part of the Tuxedo suite.


Available Versions

  • 1.3.0.
  • 1.3.3 beta.
  • 1.4.1 (default).

Execution Environment and Modules

To use tophat with the environment modules system at HPC the following commands are available:

Get module information for tophat:

$module spider tophat

Load the default application module:

$module load tophat

The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:

  • HPC_TOPHAT_DIR - directory where tophat is located.
  • HPC_TOPHAT_BIN - executable directory
  • HPC_TOPHAT_DOC - documents directory