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tophat website  

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.

Required Modules

modules documentation


  • tophat

System Variables

  • HPC_{{#uppercase:tophat}}_DIR - installation directory
  • HPC_TOPHAT_BIN - executable directory
  • HPC_TOPHAT_DOC - documents directory

How To Run

Note: If your data is compressed your job script should add another ppn to accommodate the external gzip process tophat will run. To be safe, add another ppn in any case.


  • Validated 4/5/2018