[IGBF-4018] Add Dama dama genome to IGB - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Minor
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
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Story Points:
1
Epic Link:
Add genomes requested during SDB
Sprint:
Winter 1, Spring 1, Spring 2, Spring 3

Description

Task: Add the Dama dama (fallow deer) genome and annotation to IGB. Current Dama dama genome version provided by NCBI RefSeq: GCF_033118175.1.

Dama dama (ASM3311817v1)(Nov 2023) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_033118175.1/

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relates to

IGBF-4010 Create documentation for adding NCBI genomes to IGB Quickload

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Paige Kulzer added a comment - 14/Jan/25 11:12 AM

Below is an outline of the steps I followed to create the Dama dama Quickload:
1. Convert genome .fna to .2bit

./faToTwoBit GCF_033118175.1_ASM3311817v1_genomic.fna D_dama_Nov_2023.2bit

2. Create genome.txt and check to make sure it's ordered in a way that makes sense

./twoBitInfo D_dama_Nov_2023.2bit genome.txt
cat genome.txt

3. Convert annotations .gff to .bed

~/Documents/Repos/genomesource/gff3ToBedDetail.py -g genomic.gff -b D_dama_Nov_2023_ncbiRefSeq.bed

4. Sort, gzip, and tabix the .bed file

sort -k1,1 -k2,2n D_dama_Nov_2023_ncbiRefSeq.bed | bgzip > D_dama_Nov_2023_ncbiRefSeq.bed.gz
tabix -0 -s 1 -b 2 -e 3 D_dama_Nov_2023_ncbiRefSeq.bed.gz

5. Sanity check the .bed and .2bit files - Add the .2bit file as a reference, then drag/drop the .bed file into IGB. Confirm that gene models are present, labeled correctly, and the chromosomes listed are in a logical order. Also check that no error messages are present in the Log.

6. Make a new genome directory and create annots.xml

cd ~/Documents/Repos/quickload

mkdir D_dama_Nov_2023
cd D_dama_Nov_2023

cp ../C_teleta_Jan_2013/annots.xml .
nano annots.xml

7. Add Dama dama to contents.txt and .htaccess

cd ..
nano contents.txt
nano .htacess

8. Add Dama dama to species.txt and synonyms.txt

nano species.txt
nano synonyms.txt

Link to a zipped copy of the quickload on Google Drive: https://drive.google.com/drive/folders/1bFRx4PqldxNf400n7Vr9SD_dNeNmtpvk?usp=drive_link

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Paige Kulzer added a comment - 14/Jan/25 11:12 AM Below is an outline of the steps I followed to create the Dama dama Quickload: 1. Convert genome .fna to .2bit ./faToTwoBit GCF_033118175.1_ASM3311817v1_genomic.fna D_dama_Nov_2023.2bit 2. Create genome.txt and check to make sure it's ordered in a way that makes sense ./twoBitInfo D_dama_Nov_2023.2bit genome.txt cat genome.txt 3. Convert annotations .gff to .bed ~/Documents/Repos/genomesource/gff3ToBedDetail.py -g genomic.gff -b D_dama_Nov_2023_ncbiRefSeq.bed 4. Sort, gzip, and tabix the .bed file sort -k1,1 -k2,2n D_dama_Nov_2023_ncbiRefSeq.bed | bgzip > D_dama_Nov_2023_ncbiRefSeq.bed.gz tabix -0 -s 1 -b 2 -e 3 D_dama_Nov_2023_ncbiRefSeq.bed.gz 5. Sanity check the .bed and .2bit files - Add the .2bit file as a reference, then drag/drop the .bed file into IGB. Confirm that gene models are present, labeled correctly, and the chromosomes listed are in a logical order. Also check that no error messages are present in the Log. 6. Make a new genome directory and create annots.xml cd ~/Documents/Repos/quickload mkdir D_dama_Nov_2023 cd D_dama_Nov_2023 cp ../C_teleta_Jan_2013/annots.xml . nano annots.xml 7. Add Dama dama to contents.txt and .htaccess cd .. nano contents.txt nano .htacess 8. Add Dama dama to species.txt and synonyms.txt nano species.txt nano synonyms.txt Link to a zipped copy of the quickload on Google Drive: https://drive.google.com/drive/folders/1bFRx4PqldxNf400n7Vr9SD_dNeNmtpvk?usp=drive_link

4 older comments

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Nowlan Freese added a comment - 22/Jan/25 12:17 PM

Looks good, ready for pull request.

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Nowlan Freese added a comment - 22/Jan/25 12:17 PM Looks good, ready for pull request.

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Paige Kulzer added a comment - 23/Jan/25 11:43 AM

The Dama dama genome has been pushed to the SVN repo. Ready for final review!

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Paige Kulzer added a comment - 23/Jan/25 11:43 AM The Dama dama genome has been pushed to the SVN repo. Ready for final review!

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Nowlan Freese added a comment - 24/Feb/25 10:48 AM

Tested using my local copy of the SVN repo.

Gene models load correctly, able to load sequence, synonyms/species look good, Header.md looks good.

Ready to be deployed.

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Nowlan Freese added a comment - 24/Feb/25 10:48 AM Tested using my local copy of the SVN repo. Gene models load correctly, able to load sequence, synonyms/species look good, Header.md looks good. Ready to be deployed.

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Ann Loraine added a comment - 13/Mar/25 1:44 PM

Revision 225 of the svn repository is now deployed. Ready for final testing.

Request: Please check that the Web browser interface to the genome assembly directory on quickload makes sense and that all links work.

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Ann Loraine added a comment - 13/Mar/25 1:44 PM Revision 225 of the svn repository is now deployed. Ready for final testing. Request: Please check that the Web browser interface to the genome assembly directory on quickload makes sense and that all links work.

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Nowlan Freese added a comment - 14/Mar/25 11:29 AM - edited

Tested on Mac with main branch installer.

Dama dama appears in the Species dropdown with the correct synonyms.
Gene models and the sequence loads (2bit located at UCSC).
Quickload page loads, links all work.

Closing ticket

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Nowlan Freese added a comment - 14/Mar/25 11:29 AM - edited Tested on Mac with main branch installer. Dama dama appears in the Species dropdown with the correct synonyms. Gene models and the sequence loads (2bit located at UCSC). Quickload page loads, links all work. Closing ticket

People

Assignee:

Paige Kulzer

Reporter:

Paige Kulzer

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Dates

Created:

13/Dec/24 3:10 PM

Updated:

14/Mar/25 11:31 AM

Resolved:

14/Mar/25 11:30 AM