tophat.rst

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.

Versions

• 2.1.1-py27

Commands ~~~~~~~ - tophat - tophat2

Module

You can load the modules by:

module load biocontainers
module load tophat

Example job ~~~~~ .. warning:: 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