Cufflinks

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

Module file

The module file can be found in this location:

 /cm/shared/modulefiles/SHARED/

<source lang='tcl'>

1. %Module1.0#######################################################################
   1. cufflinks 2.1.1 modulefile

proc ModulesHelp { } {

       puts stderr "\tAdds cufflinks 2.1.1 to your environment"

}

module-whatis "Adds cufflinks 2.1.1 to your environment"

module load tophat/2.0.11 bowtie/2-2.2.1

set cufflinks_211_root /cm/shared/apps/SHARED/cufflinks/cufflinks-2.1.1.Linux_x86_64/

prepend-path PATH $cufflinks_211_root

</source>

Installation details

Downloaded as pre-compiled binaries on 15-03-2014:

  http://tophat.cbcb.umd.edu/downloads/tophat-2.0.11.Linux_x86_64.tar.gz

See also

• Globally installed software
• ABGC specific modules

External links

• Cufflinks home page