= Updating to Reggie 4.15 = === Update to BASE 3.11.3 === The !StringTie pipeline requires new functionality in the BASE core API. See http://base.thep.lu.se/ticket/2108. === 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. === Create a new array design === A new array design should be created for representing the data generated by the !StringTie step. The array design should have `Platform=Sequencing/StringTie`. Upload the GTF file (''gencode.v27.primary_assembly.annotation_subset_transcripttype_proteincoding.gtf'') that !StringTie uses and attach is as the `GTF ref-seq` file to the new array design. Note! It may take a while to save due to parsing the GTF file. Please be patient! === Remove existing Hisat alignments === Use the '''Delete unmasked Hisat alignments''' wizard to delete existing Hisat alignments. There is no masking step before the alignment, and the genotyping is done with a shorter list (51) SNPs. Do not attempt to run the '''Genotype quality control''' wizard before the old alignments have been removed since this may lead to unpredictable results. === The QC_GenoTypeHET annotation type is no longer used === The `QC_GenoTypeHET` annotation type has been replaced with `QC_GenoTypeHET_PCT`. Once all alignments that uses this annotation has been deleted the annotation type can be removed.