TopHat

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 tophat to discover versions available and to load the application.

The application uses python/2.7.18.

If you have loaded other modules that configure the environment to use a different version of python then this will conflict with what tophat requires and you will see errors of the form:

[]$ tophat2 -h
/apps/u/opt/linux/tophat/2.1.1/tophat:224: SyntaxWarning: invalid escape sequence '\w'
  r=re.match("^#>(\w+):$", line)
  File "/apps/u/opt/linux/tophat/2.1.1/tophat", line 1003
    except getopt.error, msg:
           ^^^^^^^^^^^^^^^^^
SyntaxError: multiple exception types must be parenthesized

To resolve perform a module purge and only have tophat running within a session.

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:

[salexan5@mblog2 5.0.3]$ tophat2 -h
tophat:
TopHat maps short sequences from spliced transcripts to whole genomes.
...
    -p/--num-threads               <int>       [ default: 1                   ]
...