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.
License
Free to use and open source under Boost Software License 1.0.
Available
- Roihu: 2.1.2, via the
bio-appsmodule.
Usage
TopHat is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the TopHat module:
Tophat jobs should be run as batch jobs. Below is a sample batch job file for running a TopHat job on Roihu:
#!/bin/bash
#SBATCH --job-name=tophat
#SBATCH --account=<project>
#SBATCH --output=out_%j.txt
#SBATCH --error=err_%j.txt
#SBATCH --partition=small
#SBATCH --time=24:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=16G
module load bio-apps/v202603
module load tophat/2.1.2
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 creating a batch job script for Roihu for more information about running batch jobs.