Tophat

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Category

Bioinformatics, Aligner

Description

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
2.0.13

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

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

Please note that this page refers to installations from the old software stack. There are two software stacks on Euler. Newer versions of software are found in the new software stack.

How to submit a job

You can submit a tophat job in batch mode with the following command:
sbatch [Slurm options] --wrap="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 [Slurm options] with Slurm parameters for the resource requirements of the job. Please find a documentation about the parameters of sbatch 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.

License information

Artistic license 1.0

Links

https://ccb.jhu.edu/software/tophat/index.shtml

https://en.wikipedia.org/wiki/TopHat_(bioinformatics)