Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Epic Link:
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Sprint:Fall 4 2021 Sep 27 - Oct 8
Description
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific.
Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to:
GENOTYPE_TREATMENT_REPLICATE
Genotypes:
- VF36 (wildtype)
- F3H-OX3 (F3H over-expressing line 3)
- F3H-OX4 (F3H over-expressing line 4)
- are (mutant, anthocyanin reduced)
Treatments (duration 2 hours):
- 28 degrees C for 2 hours (control), harvested at 120 minutes
- 28 degrees C for 30 minutes, then shifted to 34 C (treatment), harvested at 120 minutes
Sample codes:
genotype: VF36, F3H-OX3, F3H-OX4
treatment: C and T
replicate: R1, R2, R3
Attachments
Issue Links
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2323 [ 18477 ] |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control) * 28 degrees C then shifted 34 C (treatment) Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (mutant) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control) * 28 degrees C then shifted 34 C (treatment) Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
| Description |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (mutant) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control) * 28 degrees C then shifted 34 C (treatment) Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE 4 Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (anthocyanin reduced) 2 Treatments: * 28 degrees C for 2 hours (control), harvested at 120 minutes * 28 degrees C then shifted 34 C after 30 minutes (treatment), harvested at 120 minutes Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
| Description |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE 4 Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (anthocyanin reduced) 2 Treatments: * 28 degrees C for 2 hours (control), harvested at 120 minutes * 28 degrees C then shifted 34 C after 30 minutes (treatment), harvested at 120 minutes Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (mutant) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control) * 28 degrees C for 30 minutes, then shifted to 34 C (treatment) Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
| Description |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (mutant) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control) * 28 degrees C for 30 minutes, then shifted to 34 C (treatment) Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (mutant, anthocyanin reduced) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control) * 28 degrees C for 30 minutes, then shifted to 34 C (treatment) Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
| Description |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (mutant, anthocyanin reduced) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control) * 28 degrees C for 30 minutes, then shifted to 34 C (treatment) Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
The first run of the rnaseq pipeline used a samples.csv file as input that indicated the incorrect strand.
The protocol used to synthesis the libraries (see attached) was not strand-specific. Also, the sample name prefixes are a bit awkward and long. Since every sample name contains the letters "120min" let's shorten the prefixes to: GENOTYPE_TREATMENT_REPLICATE Genotypes: * VF36 (wildtype) * F3H-OX3 (F3H over-expressing line 3) * F3H-OX4 (F3H over-expressing line 4) * are (mutant, anthocyanin reduced) Treatments (duration 2 hours): * 28 degrees C for 2 hours (control), harvested at 120 minutes * 28 degrees C for 30 minutes, then shifted to 34 C (treatment), harvested at 120 minutes Sample codes: genotype: VF36, F3H-OX3, F3H-OX4 treatment: C and T replicate: R1, R2, R3 |
| Summary | Re-run nf-core/rnaseq using proper strand designation and better sample prefex | Re-run nf-core/rnaseq using proper strand designation and better sample prefix |
| Link | This issue relates to IGBF-2971 [ IGBF-2971 ] |
| Attachment | LibrarySynthesisProtocol.pdf [ 16790 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |