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Overview
TopHat: 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.
Using
Use the module name amber
tophat
to discover versions available and to load the application.
Note | ||
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The application uses If you have loaded other modules that configure the environment to use a different version of python then this will conflict with what
To resolve perform a |
Multicore
Some of the tophat
set of commands can use multiple cores. Please specifically look at each command to see whether this is enabled. For example:
Code Block |
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[salexan5@mblog2 5.0.3]$ tophat2 -h
tophat:
TopHat maps short sequences from spliced transcripts to whole genomes.
...
-p/--num-threads <int> [ default: 1 ]
... |