= 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 and files (in the BASE filesystem) that are related to them. There is no masking step before the alignment, and the genotyping is done with a shorter list (51) SNPs. Use the '''Stray files wizard''' to delete files from the file server. 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.