= Updating to Reggie 4.23 = TODO - when to do the different steps! TODO - state requirements: no current sequencing or secondary analysis jobs == 1. Set value for Pipeline annotation on existing items == Almost all existing items from Library and downstream must be given a value for the **Pipeline** annotation. The table below specifies the value to set for the Pipeline annotation for different types of items. It should be possible to do a manual batch export/import for each row or groups of rows. || **Item type** || **Subtypes** || **Additional filter** || **Pipeline value** || || Extract || Library, !PooledLibrary, !PooledLibraryAliquot || - || RNAseq || || Physical bioassay || !FlowCell || - || RNAseq || || Derived bioassay || !SequencingRun, !DemuxedSequences, !MergedSequences || - || RNAseq || || Derived bioassay || !MaskedSequences, !AlignedSequences || Job type = !HisatAlign || RNAseq/Hisat/StringTie || || Derived bioassay || !MaskedSequences, !AlignedSequences || Job type <> !HisatAlign || RNAseq/Legacy || || Raw bioassay || Cufflinks || - || RNAseq/Legacy || || Raw bioassay || !StringTie || - || RNAseq/Hisat/StringTie || || Protocol || Demuxing, Merging || - || RNAseq || || Software || Demuxing, Merging || - || RNAseq || == 2. Other updates to existing items == Existing Hardware items of type=Sequencer should be updated with a value for the **!FlowCellType** annotation. It should be either !NextSeq or !HiSeq. == 3. New items that should be created == || **Item type** || **Subtypes** || **Additional settings** || **Comment** || || Protocol || DNANormalization || !TargetAmount, !TargetMinimalAmount, !TargetVolume, MIPS_Pool || The protocol to use for normalizing DNA that should go into the MIPs pipeline. || || Protocol || Library preparation || !LibPrepTarget=MIPs || One or more protocols that will appear in the "MIPs library registration" wizard || || Protocol || Pooling || !LibPrepTarget=MIPs || One or more protocols that will appear in the MIPs pooling wizard || || Protocol || Demuxing || Pipeline=MIPs || One or more protocols that will appear in the MIPs demux wizard (demux section) || || Software || Demuxing || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard (demux section) || || Protocol || Merging || Pipeline=MIPs || One or more protocols that will appear in the MIPs demux wizard (merge section) || || Software || Merging || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard (merge section) || == 4. Barcode templates == Most of the barcode information (such as the sequences, positions, etc.) should be available as a file that can be used with batch importers. Some steps need to be done manually. 1. A barcode templates is represented as a **Bioplate** item where each coordinate is linked to a **Tag** item. Start by manually creating the required number of bioplates. They should have the following values: || **Bioplate type** || !BarcodeTemplate || || **Plate geometry** || 96-well (8x12) || || **Pipeline** (annotation) || MIPs || 2. Import/create **Tag** items from file using the batch **Tag importer** and then add annotations with the **Annotation importer**. The following values are required: || **Name** || Name of the barcode/tag which must be unique || || **Pipeline** || All items should be set to `MIPs` || || **!BarcodeSequence** || The barcode sequence for the first index read || || **BarcodeSequence2** || The barcode sequence for the second index read || 3. Link the barcodes to templates. This is done by creating (virtual) extracts and link them with tags and positions on one of the bioplates created in the first step. It should be possible to do this with the batch **Extract importer**: || **Name** || Name of the extract (recommended to be the same as the name of the Tag) || || **Tag** || Name of the tag || || **Bioplate** || Name of the template bioplate || || **Biowell row** || Row coordinate on the template bioplate (A-H) || || **Biowell column || Column coordinate on the template bioplate (1-12) ||