[IGBF-1617] Update human genome annotation - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: 9.1.6 Major Release
Labels:
None

Story Points:
1
Epic Link:
Improve IGB for users
Sprint:
Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Fall 3: Oct 12 - Oct 23

Description

Situation: A user commented on the lack of variants for the Androgen Receptor (AR) gene in humans. This paper discusses several variants, while the current human annotation for hg19 and hg38 has only two variants. We would like to add an additional annotation to mirror what is in NCBI .

Task: Add the RefSeq annotation for hg19 and hg38 for humans. Need to find additional gene name information for field 13 and 14.

Attachments

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Attachments

MetadataCompare.png
352 kB
20/Oct/20 5:47 PM
RefSeq_Compare.png
1.11 MB
20/Oct/20 5:47 PM
SNP(old vs new).png
1.04 MB
20/Oct/20 5:47 PM

Issue Links

relates to

IGBF-3330 Add mm39 (GRCm39) mouse genome to IGB

Closed

Activity

Ascending order - Click to sort in descending order

Nowlan Freese created issue - 05/Mar/19 3:53 PM

Nowlan Freese made changes - 05/Mar/19 4:31 PM

Field	Original Value	New Value
Description		Situation: A user commented on the lack of variants for the Androgen Receptor (AR) gene in humans. This [paper \| https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4209743/] discusses several variants, while the current human annotation for hg19 and hg38 has only two variants. We would like to add an additional annotation to mirror what is in [NCBI \| https://www.ncbi.nlm.nih.gov/gene?term=NM_000044]. Task: Add the RefSeq annotation for [hg19 \| https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=714371239_WYTO2Q8Fcz5YyPSahitD4r0CxPAg&boolshad.hgta_printCustomTrackHeaders=0&hgta_ctName=tb_knownGene&hgta_ctDesc=table+browser+query+on+knownGene&hgta_ctVis=pack&hgta_ctUrl=&fbQual=whole&fbUpBases=200&fbExonBases=0&fbIntronBases=0&fbDownBases=200&hgta_doMainPage=cancel] and [hg38 \| https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=714371239_WYTO2Q8Fcz5YyPSahitD4r0CxPAg&clade=mammal&org=Human&db=hg38&hgta_group=genes&hgta_track=refSeqComposite&hgta_table=ncbiRefSeq&hgta_regionType=genome&hgta_outputType=bed&hgta_outFileName=ncbi.bed] for humans. Need to find additional gene name information for field 13 and 14.

Ann Loraine made changes - 27/Aug/19 4:58 PM

Workflow

Loraine Lab Workflow [ 18338 ]

Fall 2019 Workflow Update [ 18958 ]

Ann Loraine made changes - 16/Oct/19 5:48 PM

Workflow	Fall 2019 Workflow Update [ 18958 ]	Revised Fall 2019 Workflow Update [ 21083 ]
Status	Open [ 1 ]	In Progress [ 3 ]

Nowlan Freese made changes - 21/May/20 10:25 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 12/Jul/20 11:04 PM

Epic Link

IGBF-1765 [ 17855 ]

Ann Loraine made changes - 12/Jul/20 11:04 PM

Sprint

Summer 4: 14 Jul - 28 Jul [ 99 ]

Ann Loraine made changes - 16/Jul/20 4:00 PM

Rank

Ranked lower

Ann Loraine made changes - 16/Jul/20 4:01 PM

Sprint

Summer 4: 14 Jul - 28 Jul [ 99 ]

Ann Loraine made changes - 16/Jul/20 4:01 PM

Rank

Ranked higher

Ann Loraine made changes - 30/Aug/20 12:35 PM

Rank

Ranked higher

Ann Loraine made changes - 15/Sep/20 7:37 AM

Sprint

Fall 1: 14 Sep - 25 Sep [ 103 ]

Ann Loraine made changes - 15/Sep/20 7:37 AM

Rank

Ranked lower

Ann Loraine made changes - 15/Sep/20 7:46 AM

Rank

Ranked higher

Ann Loraine made changes - 23/Sep/20 9:41 AM

Rank

Ranked higher

Nowlan Freese made changes - 23/Sep/20 10:12 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 23/Sep/20 10:12 AM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 25/Sep/20 9:15 AM

Status

In Progress [ 3 ]

To-Do [ 10305 ]

Ann Loraine made changes - 27/Sep/20 10:48 AM

Sprint

Fall 1: 14 Sep - 25 Sep [ 103 ]

Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct [ 103, 104 ]

Ann Loraine made changes - 27/Sep/20 10:48 AM

Rank

Ranked higher

Ann Loraine made changes - 28/Sep/20 4:27 PM

Rank

Ranked higher

Nowlan Freese made changes - 29/Sep/20 9:27 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

Nowlan Freese made changes - 02/Oct/20 2:21 PM

Assignee

Nowlan Freese [ nfreese ]

Ann Loraine [ aloraine ]

Nowlan Freese made changes - 02/Oct/20 2:21 PM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 02/Oct/20 2:21 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 02/Oct/20 2:21 PM

Status

First Level Review in Progress [ 10301 ]

Needs 1st Level Review [ 10005 ]

Nowlan Freese made changes - 02/Oct/20 2:22 PM

Status

Needs 1st Level Review [ 10005 ]

First Level Review in Progress [ 10301 ]

Nowlan Freese made changes - 02/Oct/20 2:22 PM

Status

First Level Review in Progress [ 10301 ]

Ready for Pull Request [ 10304 ]

Nowlan Freese made changes - 02/Oct/20 2:22 PM

Status

Ready for Pull Request [ 10304 ]

Pull Request Submitted [ 10101 ]

Ann Loraine made changes - 12/Oct/20 8:04 AM

Sprint

Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct [ 103, 104 ]

Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Fall 3: Oct 12 - Oct 23 [ 103, 104, 106 ]

Ann Loraine made changes - 12/Oct/20 8:04 AM

Rank

Ranked higher

Ann Loraine made changes - 13/Oct/20 6:54 AM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 13/Oct/20 6:54 AM

Status

Pull Request Submitted [ 10101 ]

Reviewing Pull Request [ 10303 ]

Ann Loraine made changes - 13/Oct/20 6:54 AM

Status

Reviewing Pull Request [ 10303 ]

Merged Needs Testing [ 10002 ]

Ann Loraine made changes - 14/Oct/20 5:08 PM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Ann Loraine made changes - 14/Oct/20 5:08 PM

Assignee

Ann Loraine [ aloraine ]

Ann Loraine made changes - 16/Oct/20 9:17 AM

Status

Post-merge Testing In Progress [ 10003 ]

Merged Needs Testing [ 10002 ]

Ann Loraine made changes - 16/Oct/20 9:18 AM

Assignee

Ann Loraine [ aloraine ]

Sai Supreeth Segu (Inactive) made changes - 20/Oct/20 10:40 AM

Assignee

Sai Supreeth Segu [ ssegu ]

Sai Supreeth Segu (Inactive) made changes - 20/Oct/20 10:40 AM

Status

Merged Needs Testing [ 10002 ]

Post-merge Testing In Progress [ 10003 ]

Sai Supreeth Segu (Inactive) made changes - 20/Oct/20 5:47 PM

Attachment		MetadataCompare.png [ 14905 ]
Attachment		SNP(old vs new).png [ 14906 ]
Attachment		RefSeq_Compare.png [ 14907 ]

Sai Supreeth Segu (Inactive) made changes - 20/Oct/20 5:47 PM

Assignee

Sai Supreeth Segu [ ssegu ]

Sai Supreeth Segu (Inactive) made changes - 21/Oct/20 10:13 AM

Resolution		Done [ 10000 ]
Status	Post-merge Testing In Progress [ 10003 ]	Closed [ 6 ]

Sai Supreeth Segu (Inactive) made changes - 21/Oct/20 10:13 AM

Assignee

Nowlan Freese [ nfreese ]

Nowlan Freese made changes - 17/Nov/20 10:24 AM

Fix Version/s

9.1.6 Major Release [ 10604 ]

Nowlan Freese made changes - 07/Jun/23 1:13 PM

Link

This issue relates to ~~IGBF-3330~~ [ ~~IGBF-3330~~ ]

People

Assignee:

Nowlan Freese

Reporter:

Nowlan Freese

Votes:

0 Vote for this issue

Watchers:

3 Start watching this issue

Dates

Created:

05/Mar/19 3:53 PM

Updated:

07/Jun/23 2:36 PM

Resolved:

21/Oct/20 10:13 AM