harrietc52
commented
1 year ago Questions
Q: CSV currently is missing every other row. Assume empty rows can just be ignored?
Q: Column D: pg/uL or ng/uL or wanting to support both? Same for Column F: pmole/L or nmole/L.
Q: Will all CSV's have the same columns? If not, what is the full list of potential columns? Which columns are required, or not? e.g Size Threshold (b.p.) and GQN are sometimes empty. Assume these results would be ignored?
Q: "Only effective if the other important metrics are uploaded into the MLWH" (Ben F). Which other metrics? Metrics for each of the existing columns in attached CSV? Or more? (clade, yield, quality, input amounts, lysis type, powermash/cryoprep, date extraction run, date sample caught, team doing extraction…)
Q: Please could there be a Description for each of the columns
Q: There are duplicate Sample ID is the same well. Is this expected? Is this the same sample with multiple different QC values, in the same well? Or is this "Sample ID" the name of the Femto trace, of which there is multiple in one well? Maybe we could rename this field? So there would be multiple Femto traces in 1 well?
Q: Are columns C - J all the QC values? What do these result represent? (Femto traces?) Are they each an individual Femto trace, or are they as a collective, represent a femto trace?
Q: Should a row only be processed if there is a Well and Sample ID provided? What identifies a row?
Q: "Whichever direction we go we’ll require a way of standardising the way we name the femto traces. Currently a free text box is used to type the name of the sample" (Ben F). Where is this current free text input to enter the "Sample ID"/ Femto trace name? What would you prefer this to be instead of a free text field? What validation/ limitations should be on this input?
Q: (Assume this is related the the above Q.) "If we wanted to upload the results to the MLWH we’d want a way of restricting how the sample is named so we can interrogate the data effectively in tableau" (Ben F). How would they want to restrict the same name, and why? Make it unique per well? How would they interrogate the data in Tableau?
Q: "Data would need to be uploaded in a consistent format e.g. always scan the tissue tube ID (FD20706843) barcode into the femto" (Ben F slides). Is another field required in the upload CSV to include Tissue Tube ID? Tractions current implementation of QC upload requires the fields Tissue Tube ID and Sanger sample ID as these are required to create the QcResult entities. Could the Tissue Tube ID be added to the CSV? Or again, what uniquely identifies a row in the CSV.
Q: "Would need to be careful the export settings don’t change e.g pg/µl>ng/µl" (Ben F). Which export settings are being referred to here? (e.g. Export to Traction or Tabluea). Currently in Tractions implementation of QC Upload, the pre defined unit of a QC Assay Type is persisted to the MLWH. We would need to ensure each possible CSV heading, is predefined in Traction config with it's singular unit.
SujitDey2022
Description
As Ben, I would like to upload Femto QC results and have them persisted in MLWH. So we can perform automated analysis on the samples. (Benefits described in comment below)
Who the primary contacts are for this work Ben Farr Hermione Blomfield-Smith Steve I Harriet C
Knowledge or Stake holders Other people that may have specific knowledge about this work or have a stake in how it is implemented. e.g. John Smith is an expert on x
Additional context or information Any other useful context or information that may be useful.