DescriptionTophat 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 jobYou 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 https://ccb.jhu.edu/software/tophat/manual.shtml for more information about the input files (<genome_index_base> <reads1_1[,...,readsN_1]> [reads1_2,...readsN_2]) that are required for running tophat.