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 <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.

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

Existing Hisat alignments should be removed. 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.