Tophat

Description

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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).

Running the application using 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