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Welcome to the wiki of GIIRA, a method for RNA-Seq driven gene finding incorporating ambiguous reads!
Please refer to the README.txt for general information and details on parameter settings.

GIIRA was designed and tested on a linux system and has the following minimim software requirements:

• Python http://www.python.org/
• Java http://www.java.com
• either the CPLEX Optimizer (http://www-01.ibm.com/software/integration/optimization/cplex-optimizer/)
  or the GLPK solver (http://www.gnu.org/software/glpk/glpk.html)

To install GIIRA, download and unpack the file GIIRA.zip, then the included GIIRA.jar is ready for use.

An example dataset is included in the directory GIIRA/example/, whereas a usage description is provided in the README.txt.

Project Members:

• Franziska Zickmann (admin)