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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 edited Mon Mar 29 2021