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Bioinformatics, Aligner


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.

Available versions (Euler, old software stack)

Legacy versions Supported versions New versions

Environment modules (Euler, old software stack)

Version Module load command Additional modules loaded automatically
2.0.13 module load legacy gcc/4.8.2 python/2.7.6 boost/1.55.0 tophat/2.0.13 openblas/0.2.13_seq

How to submit a job

You can submit a tophat job in batch mode with the following command:
bsub [LSF options] "tophat [tophat options] <genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]"
Here you need to replace [tophat options] with tophat command line options (please run tophat -h for getting a list of all command line options) and [LSF options] with LSF parameters for the resource requirements of the job. Please find a documentation about the parameters of bsub on the wiki page about the batch system. Please have a look at for more information about the input files (<genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]) that are required for running tophat.

License information

Artistic license 1.0