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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.


Free to use and open source under [Boost Software License 1.0]


Version on CSC's Servers

  • Puhti: 2.1.1
  • Chipster graphical user interface
  • FGCI: 1.3.2, 2.0.0


In Puhti tophat is initialized with command:

module load biokit
The biokit module sets up a set of commonly used bioinformatics tools, including Bowtie2, TopHat2 and Cufflinks.

Tophat jobs should be run as batch jobs. Below is a sample batch job file, for running a TopHat job in Puhti:

#SBATCH --job-name=tophat
#SBATCH --output=out_%j.txt
#SBATCH --error=err_%j.txt
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=16G
#SBATCH --time=24:00:00
#SBATCH --partition=small
#SBATCH --account=project_1234567

module load biokit
tophat -p $SLURM_CPUS_PER_TASK -o tophat_results Homo.sapiens_bwt2_index reads1.fq reads2.fq 

In the batch job example above, one task (--ntasks=1) is executed. The job uses 4 cores (--cpus-per-task=4) with 16 GB of memory (--mem=16G). The maximum duration of the job is 24 hours (--time=24:00:00).

Change --account to match your own project name.

Note that we also need to tell TopHat to use the number of cores we reserved. In Tophat this is done with the -p command line argument. We can use system variable $SLURM_CPUS_PER_TASK to automatically match the reservation made with --cpus-per-task. This way we don't need to change the command line if we change the reservation.

See the Puhti user guide for more information about running batch jobs.



Last update: October 10, 2022