ILRI Research Computing

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====== TopHat ======
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.

  * Version: 2.1.0
  * Added: July, 2015
  * Link: http://ccb.jhu.edu/software/tophat/index.shtml

=== Usage ===
  * Show all available versions of tophat<code>module avail tophat</code>
  * Load tophat module: <code>module load tophat2/2.1.0</code>

=== Installation ===
  *Tophat2 is already compiled, just download the tarball & copy content to /export/apps<code>
wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.0.Linux_x86_64.tar.gz
tar -xvf tophat-2.1.0.Linux_x86_64.tar.gz
cd tophat-2.1.0.Linux_x86_64/
sudo mkdir /export/apps/tophat2/2.1.0
sudo cp -r . /export/apps/tophat2/2.1.0/
</code>