Micro RNA sequencing

[Nicklas Nordborg]

We need to implement a set of wizard for the MicroRNA sequencing project. The starting point is from Lysate items where a new extraction will made creating RNA extracts with small RNA. The RNA is taken to library preparation and pooled with 64 extracts in a single pool. Sequencing is made with the Illumina NextSeq machine (we already have ~3 runs since before). Demuxing can probably be implemented with Picard using our existing functionality.

This ticket will handle the changes required for lab work, sequencing and demuxing. Alignment and other secondary analysis will be in another ticket.

Implementation ideas:

• A new subtype sRNA should be defined (it already exists on the production server). It should represent the extracted RNA and be linked to the Lysate. We may need a wizard to import annotations. We probably want the concentration and storage location, etc...
• A new value for the Pipeline annotation should be defined. It could work with sRNAseq? It should be used on items downstream from the sRNA items: Library, Barcode, Pool, FlowCell, SequencingRun and DemuxedSequences. (Note! We could have used the pipeline and regular RNA items instead of sRNA items but there is a lot of existing code that need to be modified to check the pipeline annotation so it is safer to introduce a new subtype)
• We need a wizard to import information about a sequencing run.
  • The 64 libraries that was pooled and their barcodes
  • The flow cell barcode

This should be enough for us to create the Library items and other intermediary items that are needed and it should be possible to start the demux after that.