Difference between revisions of "Tophat"
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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 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. | ||
Revision as of 01:54, 10 August 2012
Description
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