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MullinsLab / viroverse

a platform for the collection, storage, retrieval, and analysis of experimental data for laboratory workflows
MIT License
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Creating Multiplex Sequencing Runs that collect PCR products #16

Open silby opened 5 years ago

silby commented 5 years ago

In order to support the automatic upload of sequence data from multiplexed high-throughput sequencing (PacBio protocols in our lab specifically) we need to be able to add Multiplex Sequencing Run records that, in addition to some metadata, serve as collections of the PCR products used to prepare the sequencing library. Discovery needs to be done on what metadata is required, apart from the true basics (a scientist ID, an entry date, a name for the run).

Users must be able to create Sequencing Runs, as well as search for PCR products and add them to the run. Metadata display for PCR products in the context of the Sequencing Run display should highlight the original sample and the primer used for RT, which contains the sample barcode for sequence multiplexing.

silby commented 5 years ago

Elsewhere I summarized some subtasks:

  1. A sequencing_run table with a many-many join to pcr_product
  2. CRUD for sequencing run records
  3. UI flow for adding PCR products to a sequencing run as "products being sequenced"
  4. Business logic to verify that a sequencing run is "appropriately multiplexed", i.e. each PCR product included has a distinct sample ID primer (such as PB_A1…, PB_A2…)
silby commented 5 years ago

We solved the immediate need for the Mullins Lab in a different way (see #83), this might still be a desired improvement but it's no longer "urgent"