= Updating to Reggie 4.15 = === New !StringTie pipeline in the Hisat secondary analysis === In `reggie-config.xml` the following changes are required: * In the `` section, a `` sub-section should be added with the full `` to the !StringTie executable. * A `` section with !StringTie configuration parameters should be added. The configuration file shipped with Reggie should contain functional default values. === New annotation on feature extraction software and protocols === A new annotation type, `ExpressionType` has been added. Find existing software and protocols with `Type=Feature extraction` and set the `ExpressionType` annotation to `Cufflinks`. Create a new software and protocol item for the !StringTie pipeline. They should have `Type=Feature extraction` and `ExpressionType=StringTie`. Keep the `Add as project default` checkbox checked and the `Replace existing default` unchecked.