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Compmerge
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Compmerge is a tool that tries to solve the same problem as cuffmerge.
It is not limited to cufflinks models and transcripts, but can work with
any .gtf file.
It merges the spliced transcripts that have a compatible intron structure
and merges the monoexonic transcripts based on simple stranded overlap.
The output is a .gtf file of merged transcripts.

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Get Started Quickly With Compmerge
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Check out Compmerge from svn::

  $ svn co --username rnaguest --password rnaguest svn://svn.crg.es/big/compmerge/trunk compmerge
  $ cd compmerge