====== Cufflinks ======

**Cufflinks** is a software module available on **Comet**.

===== Cufflinks overview =====

To access **Cufflinks** on Comet, run ''module load Cufflinks''. This will load the //default// version of **Cufflinks**.

An overview of the module information is shown below (''module -r spider ^Cufflinks$''):

<code lang=text>
  Cufflinks: Cufflinks/20190706-GCC-12.3.0
    Description:
      Transcript assembly, differential expression, and differential regulation for RNA-Seq

    This module can be loaded directly: module load Cufflinks/20190706-GCC-12.3.0

    Help:
      
      Description
      ===========
      Transcript assembly, differential expression, and differential regulation for RNA-Seq
      
      More information
      ================
       - Homepage: http://cole-trapnell-lab.github.io/cufflinks/
</code>

If there are multiple versions of **Cufflinks** listed, then you can load a //specific// version as follows:
<code lang=bash>
$ module load Cufflinks/version_string
</code>

You can find the most //up to date information// whilst logged on to Comet by running ''module -r spider ^Cufflinks$''.

----

===== Cufflinks Help =====

The module **Cufflinks** has the following embedded help text (''module help Cufflinks''):

<code lang=text>Description
===========
Transcript assembly, differential expression, and differential regulation for RNA-Seq

More information
================
 - Homepage: http://cole-trapnell-lab.github.io/cufflinks/

</code>

----

===== Cufflinks Dependencies =====

The //default// version of the module **Cufflinks** has the following dependencies:

   * GCC/12.3.0
   * zlib/1.2.13-GCCcore-12.3.0
   * HTSlib/1.18-GCC-12.3.0

----

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