ceciliamattssonscilifelab commented 2 years ago

Lims Issue

Quantit protocol: AM 1843 Method - Quant-iT assay on Fluostar Omega, Atlas title: Plate Reader Qubit protocol: AM 1026 Qubit - Equipment manual, Atlas title: Qubit

List of workflows: Qubit and Quantit steps in LIMS workflows.docx

Description: Several (n=22) workflows in LIMS include either both or one of the methods for Quantit and Qubit assays. These steps needs to be updated when the method protocols are moved from AM to Atlas.

RasmusBurge-CG commented 2 years ago

Initial QC (RNA)

[x] Step 2 >> Qubit QC (RNA)

initial QC wgs v4
[x] Step 2 >> G002 – Qubit QC (DNA)
[x] Step 3 >> Quantit QC (DNA) WGS v1

Library validation QC wgs v3
[x] Step 3 >> CG002 – Qubit QC (Library Validation)
[x] Step 4 >> Qunatit QC (DNA) WGS v1

Library validation QC (RNA)
[x] Step 2 >> Quantit QC (Library Validation) (RNA)
[x] Step 3 >> Qubit QC (Library Validation) (RNA)

Library validation QC RNA (post norm)
[x] Step 2 >> Quantit QC (Library Validation) (RNA)
[x] Step 3 >> Qubit QC (Library Validation) (RNA)

Initial QC (Cov) v1
[x] Step 2 >> Qubit QC (DNA) (Cov)
[x] Step 3 >> Quantit QC(DNA) (Cov)

Library Validation QC (Cov) v1
[x] Step 2 >> Quantit QC (Library Validation) (Cov)
[x] Step 3 >> Qubit QC (Library Validation) (Cov)

Initial QC (RNA) v2
[x] Step 2 >> Quantit QC (RNA)
[x] Step 3 >> Qubit QC (RNA)

CG002 RML Initial QC. Not needed
[ ] Step 1 >> CG002 – Qubit QC RML.

CG002 Initial QC. Not needed
[ ] Step 2 >> CG002 – Reception control

Initial QC wgs v3. Not connected to a workflow.
[ ] Step 2 >> CG002 – Qubit QC (DNA)
[ ] Step 3 >> Quantit QC (DNA) WGS v1

CG002 Library validation QC. Not connected to a workflow.
[ ] Step 3 >> CG002 – Qubit QC (Library Validation)

Initial QC Microbial v3
[x] Step 1 >> CG002 - Quantit QC (DNA)

CG002 Nextera Microbial WGS. Not in use.
[ ] Step 2 >> CG002 - Quantit QC (Normalization)

CG003 Nextera Microbial WGS. Not in use.
[ ] Step 2 >> CG002 - Quantit QC (Normalization)

Microbial Library Validation QC v3
[x] Step 2 >> CG002 - Quantit QC (Library Validation)

Initial QC TWIST v3
[x] Step 2 >> Qubit QC (DNA) TWIST
[x] Step 3 >> Quantit QC (DNA) TWIST

Library Validation QC TWIST (post hyb)
[x] Step 2 >> Qubit QC (Library Validation) TWIST
[x] Step 3 >> Quantit QC (Library Validation) TWIST

Library Validation QC TWIST (post hyb) v2. Not in use.
[ ] Step 1 >> Qubit QC (Library Validation) TWIST
[ ] Step 2 >> Quantit QC (Library Validation) TWIST

Library Validation QC TWIST (post norm)
[x] Step 2 >> Qubit QC (Library Validation) TWIST
[x] Step 3 >> Quantit QC (Library Validation) TWIST

Library Validation QC TWIST v2
[x] Step 2 >> Qubit QC (Library Validation) TWIST
[x] Step 3 >> Quantit QC (Library Validation) TWIST

Initial QC (Dev) v3
[x] Step 3 >> Qubit QC (DNA) (Dev)
[x] Step 4 >> Quantit QC (DNA) (Dev)

Library Validation QC (Dev) v3
[x] Step 3 >> Qubit QC (Library Validation) (Dev)
[x] Step 4 >> Quantit QC (DNA) (Dev)

RasmusBurge-CG commented 2 years ago

https://github.com/Clinical-Genomics/atlas/pull/783

RasmusBurge-CG commented 1 year ago

Remove 1843 and 1026

Initial QC (RNA)

[ ] Step 2 >> Qubit QC (RNA)

initial QC wgs v4
[x] Step 2 >> G002 – Qubit QC (DNA)
[x] Step 3 >> Quantit QC (DNA) WGS v1

Library validation QC wgs v3
[x] Step 3 >> CG002 – Qubit QC (Library Validation)
[x] Step 4 >> Qunatit QC (DNA) WGS v1

Library validation QC (RNA)
[x] Step 2 >> Quantit QC (Library Validation) (RNA)
[x] Step 3 >> Qubit QC (Library Validation) (RNA)

Library validation QC RNA (post norm)
[x] Step 2 >> Quantit QC (Library Validation) (RNA)
[x] Step 3 >> Qubit QC (Library Validation) (RNA)

Initial QC (Cov) v1
[x] Step 2 >> Qubit QC (DNA) (Cov)
[x] Step 3 >> Quantit QC(DNA) (Cov)

Library Validation QC (Cov) v1
[x] Step 2 >> Quantit QC (Library Validation) (Cov)
[x] Step 3 >> Qubit QC (Library Validation) (Cov)

Initial QC (RNA) v2
[x] Step 2 >> Quantit QC (RNA)
[x] Step 3 >> Qubit QC (RNA)

CG002 RML Initial QC
[ ] Step 1 >> CG002 – Qubit QC RML

CG002 Initial QC
[ ] Step 2 >> CG002 – Reception control

Initial QC wgs v3
[ ] Step 2 >> CG002 – Qubit QC (DNA)
[ ] Step 3 >> Quantit QC (DNA) WGS v1

CG002 Library validation QC
[ ] Step 3 >> CG002 – Qubit QC (Library Validation)

Initial QC Microbial v3
[x] Step 1 >> CG002 - Quantit QC (DNA)

CG002 Nextera Microbial WGS
[ ] Step 2 >> CG002 - Quantit QC (Normalization)

CG003 Nextera Microbial WGS
[ ] Step 2 >> CG002 - Quantit QC (Normalization)

Microbial Library Validation QC v3
[x] Step 2 >> CG002 - Quantit QC (Library Validation)

Initial QC TWIST v3
[x] Step 2 >> Qubit QC (DNA) TWIST
[x] Step 3 >> Quantit QC (DNA) TWIST

Library Validation QC TWIST (post hyb)
[x] Step 2 >> Qubit QC (Library Validation) TWIST
[x] Step 3 >> Quantit QC (Library Validation) TWIST

Library Validation QC TWIST (post hyb) v2
[ ] Step 1 >> Qubit QC (Library Validation) TWIST
[ ] Step 2 >> Quantit QC (Library Validation) TWIST

Library Validation QC TWIST (post norm)
[x] Step 2 >> Qubit QC (Library Validation) TWIST
[x] Step 3 >> Quantit QC (Library Validation) TWIST

Library Validation QC TWIST v2
[x] Step 2 >> Qubit QC (Library Validation) TWIST
[x] Step 3 >> Quantit QC (Library Validation) TWIST

Initial QC (Dev) v3
[x] Step 3 >> Qubit QC (DNA) (Dev)
[x] Step 4 >> Quantit QC (DNA) (Dev)

Library Validation QC (Dev) v3
[x] Step 3 >> Qubit QC (Library Validation) (Dev)
[x] Step 4 >> Quantit QC (DNA) (Dev)

RasmusBurge-CG commented 1 year ago

Hej @ceciliamattssonscilifelab! You can now deprecate the documents in AM and remove the WIP in Atlas. Let me know when you are done :)

RasmusBurge-CG commented 1 year ago

Hi @susannemaner! I saw that you were assigned here, maybe you can deprecate the AM document? :)

RasmusBurge-CG commented 1 year ago

This task is finished.

Clinical-Genomics / cg_lims

Qubit and Quant-iT updates (Atlas move) #302

Lims Issue

Remove 1843 and 1026