Details
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Type:
Updated Genome
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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: 9.1.0 Major Release
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Labels:
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Story Points:0.25
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Epic Link:
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Sprint:Sprint 33, Sprint 34, Winter 2018 Sprint 2
Description
Zebrafish is one of the primary model organisms being studied by researchers. In September 2014 a new version of the genome was released. This new genome version needs to be added to IGB Quickload.
Attachments
Issue Links
- relates to
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IGBF-3330 Add mm39 (GRCm39) mouse genome to IGB
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- Closed
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-236 [ 15233 ] |
| Rank | Ranked higher |
| Assignee | David Norris [ dcnorris ] | Ann Loraine [ aloraine ] |
| Story Points | 0.25 |
| Sprint | Backlog Grooming Meeting [ 30 ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Sprint | Backlog Grooming Meeting [ 30 ] | Backlog Grooming Meeting 2 [ 31 ] |
| Sprint | Sprint 24 [ 31 ] | Backlog Grooming Meeting [ 32 ] |
| Sprint | Backlog Grooming Meeting [ 32 ] | Sprint 25 [ 34 ] |
| Rank | Ranked lower |
| Rank | Ranked higher |
| Sprint | Backlog Grooming Meeting [ 34 ] | Backlog Grooming Meeting 2 [ 35 ] |
| Rank | Ranked lower |
| Sprint | Backlog Grooming Meeting [ 35 ] | Sprint 27 [ 36 ] |
| Sprint | Backlog Grooming [ 36 ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Sprint | Sprint 33 [ 41 ] |
| Rank | Ranked lower |
| Sprint | Sprint 33 [ 41 ] | Sprint 33, Sprint 34 [ 41, 42 ] |
| Rank | Ranked higher |
| Sprint | Sprint 33, Sprint 34 [ 41, 42 ] | Sprint 33, Sprint 34, Sprint 35 [ 41, 42, 43 ] |
| Rank | Ranked higher |
| Sprint | Sprint 33, Sprint 34, Sprint 35 [ 41, 42, 43 ] | Sprint 33, Sprint 34 [ 41, 42 ] |
| Rank | Ranked lower |
| Assignee | Ann Loraine [ aloraine ] |
| Epic Link | IGBF-236 [ 15233 ] |
| Sprint | Sprint 33, Sprint 34 [ 41, 42 ] | Sprint 33, Sprint 34, Winter 2018 Sprint 2 [ 41, 42, 57 ] |
| Rank | Ranked higher |
| Assignee | Jill Jenkins [ jill ] |
| Description |
Zebrafish is one of the primary model organisms being studied by researchers. In September 2014 a new version of the genome was released. This new genome version needs to be added to IGB Quickload.
The new genome can be found here: http://hgdownload.soe.ucsc.edu/goldenPath/danRer10/bigZips/ The new annotation can be found at the UCSC table browser: https://genome.ucsc.edu/cgi-bin/hgTables There are four different annotation files for this genome. I assume refseq is the default genome, however, it would be best to have the other three annotations as well. |
Zebrafish is one of the primary model organisms being studied by researchers. In September 2014 a new version of the genome was released. This new genome version needs to be added to IGB Quickload.
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| Summary | Add new Zebrafish genome | Add new zebrafish genome |
| Status | Open [ 1 ] | In Progress [ 3 ] |
| Labels | Intermediate |
| Epic Link | IGBF-1478 [ 17563 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Jill Jenkins [ jill ] |
I have added the May 2017 assembly as per the user guide & tested in IGB.
| Status | Needs 1st Level Review [ 10005 ] | Reviewing [ 10301 ] |
| Assignee | Ann Loraine [ aloraine ] |
Committed D_rerio_May_2017 changes to subversion repo.
Updated on:
- renci host
- uncc host
- aws host
| Resolution | Done [ 10000 ] | |
| Status | Reviewing [ 10301 ] | Closed [ 6 ] |
Re-assign to original developer
| Assignee | Ann Loraine [ aloraine ] | Jill Jenkins [ jill ] |
| Workflow | Loraine Lab Workflow [ 16053 ] | Fall 2019 Workflow Update [ 20719 ] |
| Workflow | Fall 2019 Workflow Update [ 20719 ] | Revised Fall 2019 Workflow Update [ 21671 ] |
| Fix Version/s | 9.1.0 Major Release [ 10601 ] |
Follow this guide:
"Add a new UCSC-managed genome to IGB Quickload"
in Bioinformatics Data Manager google drive folder