wiki:net.sf.basedb.reggie.notes213

Version 5 (modified by Nicklas Nordborg, 6 years ago) (diff)

Adding note about fixing PoolConc? annotations

Updating to Reggie 2.13

IMPORTANT! Before installing this update, there are a number of things that need to be checked and manually fixed!!!

1. Make sure that pools have been registered

Make sure that all created pools have been completed in the lab and registered. Eg. the Lab protocols for pooling and Register pooled libraries wizards should display (0) items waiting for registration. Otherwise the lab protocols will show incorrect mixing values.

2. Flag some libraries and their parent RNA item

Due to a bug (see #508), libraries which got a Qubit concentration measurement of 0 ng/µl have been left in a dead end state. To ensure that new RNA is extracted in the future, a flag must be set manually and the parent RNA items must be added to the Flagged RNA list.

  1. To find the libraries in question go to the Biomaterial LIMS->Extracts page and filter on Type=Library and CA_Molarity=0.
  2. Edit each library item and set the annotation: Flag=ExcludedFromPool.
  3. Find the parent RNA item for each library and set the annotation: Flag=ExcludedFromPool.
  4. Add all parent RNA items to the Flagged RNA biomaterial list.
  5. Check that the selection list in the Create pooled libraries no longer include already registered library plates.

3. Fix PoolConc values for all *.dil extracts

Due to a bug (see #507), all *.dil extracts have been registered with an incorrect value for the PoolConc annotation. This need to be fixed by a manual export/import procedure.

  1. To find the libraries in question go to the Biomaterial LIMS->Extracts page and filter on name=%.dil.
  2. To avoid rounding errors in the exported data go to BASE->Preferences and set Decimals=all.
  3. Use the Table exporter plug-in to export a tab-separated file with Name and Original quantity columns.
  4. Download the exported file to your computer and open in a spreadsheet program.
  5. Add a new column PoolConc and use the following formula to calculate the values: =5 * <quantity> / 1000
  6. Save the results as a tab-separated file and upload it to BASE.
  7. Use the annotation importer to update the PoolConc values.