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

• Show all available versions of tophat

  module avail tophat

• Load tophat module:

  module load tophat2/2.1.0

• Tophat2 is already compiled, just download the tarball & copy content to /export/apps

  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/