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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.

Usage

  • Show all available versions of tophat
    module avail tophat
  • Load tophat module:
    module load tophat2/2.1.0

Installation

  • 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/
tophat-software.txt · Last modified: 2015/07/23 12:38 by joguya