Opened 8 years ago

Closed 8 years ago

#472 closed task (fixed)

Export data to files needed for library preparation

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v2.12
Component: net.sf.basedb.reggie Keywords:
Cc:

Description (last modified by Nicklas Nordborg)

Caliper and Qubit are used for quality control and measuring concentrations, fragment lengths, etc. Since we need to import data as annotations later, we'll probably want some files to feed the other software.

The following files are needed:

  • Sample name CSV for Caliper
  • Run parameters for Caliper
  • Sample names for Qubit (manually edited)

Files for the Caliper are probably similar to what is produced for RNAQC (see #365, #366 and #370). Settings are different and we need two variants. Once variant when 96-well plates are used and one variant when 384-well plates are used. In the latter case coordinates should be re-mapped to only use every other well (eg. 1, 3, 5, A, C, E, etc).

Since the Qubit doesn't have much support for files, the file generated for Qubit is a template that is manually filled in and uploaded to BASE after all extracts have been processed.

Change History (8)

comment:1 Changed 8 years ago by Nicklas Nordborg

Status: newassigned

comment:2 Changed 8 years ago by Nicklas Nordborg

(In [1896]) References #472: Export data to files needed for library preparation

Created new plug-in CaliperLibPrepParametersExporter. It is very similar to the existing CaliperRunParametersExporter, except that it should have different default value (todo) and doesn't use the HiSense option for filtering on extracts to include.

comment:3 Changed 8 years ago by Nicklas Nordborg

(In [1900]) References #472: Export data to files needed for library preparation

Added an export plug-in that generate a tab-separated file for the Qubit. The operator should add concentration measurements to this file and then upload to BASE (upload not yet implemented).

Added support for remapping 96 to 384 wells when exporting files for Caliper. However, the importer doesn't support this yet.

Changed default values for the CaliperLibPreprParametersExporter to what is currently used in the lab. Still need correct plate name for 384 plates.

comment:4 Changed 8 years ago by Nicklas Nordborg

(In [1901]) References #472: Export data to files needed for library preparation

Changed name of 384 plate to 'BioRad? Hard-shell 384'.

comment:5 Changed 8 years ago by Nicklas Nordborg

Description: modified (diff)

comment:6 Changed 8 years ago by Nicklas Nordborg

(In [1925]) References #472, #473 and #479. Added QubitConcAfterSpeedVac annotation which should be used for Qubit concentration measurements after SpeedVac?. The original Qubit concentration should always be stored in the QubitConc annotation.

The exported template file entering Qubit concentration values have been modified so that it is possible to enter both values. The test data file has been updated and a few entries now have two values.

The importer have been modified to check for both values and use the latest in when calculating molarity, original quantity, etc.

The pooling lab protocol have been updated to check if QubitConcAfterSpeedVac annotation exists or not.

comment:7 Changed 8 years ago by Nicklas Nordborg

(In [1930]) References #472 and #473. Use 'ng/ml' in Qubit files since that is what is shown in the display on the Qubit. The importer converts to 'ng/µl'.

comment:8 Changed 8 years ago by Nicklas Nordborg

Resolution: fixed
Status: assignedclosed
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