tophat
Link to section 'Introduction' of 'tophat' Introduction
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.
For more information, please check its website: https://biocontainers.pro/tools/tophat and its home page: https://ccb.jhu.edu/software/tophat/index.shtml.
Link to section 'Versions' of 'tophat' Versions
- 2.1.1-py27
Link to section 'Commands' of 'tophat' Commands
- tophat
- tophat2
Link to section 'Module' of 'tophat' Module
You can load the modules by:
module load biocontainers
module load tophat
Link to section 'Example job' of 'tophat' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run TopHat on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=tophat
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers tophat
tophat -r 20 test_ref reads_1.fq reads_2.fq