Updating to Reggie 4.15

New StringTie pipeline in the Hisat secondary analysis

In reggie-config.xml the following changes are required:

• In the <programs> section, a <stringtie> sub-section should be added with the full <path> to the StringTie executable.
• A <stringtie> 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.