wiki:net.sf.basedb.reggie/notes423

Version 2 (modified by Nicklas Nordborg, 10 months ago) (diff)

Added instructions for creating barcode templates

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 TODO
Derived bioassay MaskedSequences, AlignedSequences Job type <> HisatAlign Legacy
Raw bioassay Cufflinks - Legacy
Raw bioassay StringTie - TODO
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
  1. 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
  1. 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)