Skip to content


TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultra-fast short read mapping program Bowtie.

TopHat is available as a module on Apocrita.


To run the default version of TopHat, simply load the tophat module:

$ module load tophat
$ tophat --help

TopHat maps short sequences from spliced transcripts to whole genomes.

    tophat [options] <bowtie_index> <reads1[,reads2,...]> [reads1[,reads2,...]] \
                                    [quals1,[quals2,...]] [quals1[,quals2,...]]

For full usage documentation, run tophat --help.

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load tophat

tophat indexDir R1_samples.txt R2_samples.txt