DPL-263 - As a Heron lab user I would like to be able to upload Heron qPCR quants so I can see the concentrations in Limber (C=M, V=4)
stevieing opened this issue · comments
User story
Currently qPCR quants are done manually and analysed in a spreadsheet. Thhis means that there is no concentration in Limber and they can't be validated. Heron qPCR results should be able to be uploaded to quanthub so the quants are stored in the warehouse for analysis and can be seen in Limber to validate concentrations.
Who are the primary contacts for this story
Sara / Scott G
Acceptance criteria
To be considered successful the solution must allow:
- There should be a Heron qPCR quant type
- There should be a different dilution factor than for standard qPCR - 0.000001424
- concentration in molarity by taking the median of n=8 replicates and multiplied by dilution factor
- the plate layout should max 8 samples, n=8 replicates in 4x2 blocks (plate map below)
- the quant should be able to be exported to Sequencescape and in turn the warehouse
- Lab users should be able to see those concentrations in Limber
Dependencies
This story is blocked by the following dependencies:
- #<issue_no.>
- sanger/#<issue_no.>
References
This story has a non-blocking relationship with:
- #<issue_no.>
- sanger/#<issue_no.>
Additional context
Add any other context or screenshots about the feature request here.
Plate map:
| Wells in Copycount output | Source well of 96-well plate |
|---|---|
| A1-A4,B1-B4 | A1 |
| C1-C4,D1-D4 | B1 |
| E1-E4,F1-F4 | C1 |
| G1-G4,H1-H4 | D1 |
| I1-I4,J1-J4 | E1 |
| K1-K4,L1-L4 | F1 |
| M1-M4,N1-N4 | G1 |
| O1-O4,P1-P4 | H1 |
Example output file:
HT_132817_2897_2945_2956_HERON_16_2_22_results.csv
Outstanding questions:
- currently the plate barcode is ht_nnnnnn_* - does it need to stay that way. If so we need to add extra functionality.
Recommended tasks:
- Add the heron qPCR quant type
- Add the heron qPCR well map
- Add the conversion factor for heron qPCR
- Add an e2e test for heron qPCR (partially done - can't finish until outstanding questions have been answered).
Meeting (16/03):
- we could change the lightcycler output to add the tube barcodes
- There are two types of output from the opycoun server
- We could use a combination of those spreadsheets to provide the data we need
- This would require R&D input to create a new protocol for the lightcycler
Things to clarify:
- How big a piece of work is this for R&D
- How big a piece of work is this for PSD
- Is it a priority
HT134961_972_001_004_HERON_10_03_22_replicateSets.csv
HT134961_972_001_004_HERON_10_03_22_results.csv
Closed as not needed