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

Testing on Mac
Able to load sequence, annotations appear on chromosomes.

A few small issues:

• Check HEADER.md - there is a line that refers to H_vulgaris_Apr_2024.2bit
• I'm seeing some additional text that should probably be removed or replaced in the bed file. For example, I would not expect to see the "gene-" or the "rna-" before the title/id/name. I'm also seeing the %2C in the description of some genes, which should be replaced with a comma.
  • title: gene-SORL1
  • id: rna-XM_061146202.1
  • name: rna-XM_061146202.1
• There was no contents.txt, species.txt, or synonyms.txt in the zipped copy on Google Drive so I was not able to check that the species name was appearing as expected in the dropdown.

Thanks for catching all of this Dr. Freese! I will update the documentation I've created as part of IGBF-4010 so that I make sure to check for issues like this in the future.

I updated HEADER.md to remove any mention of the Hydra vulgaris Quickload. I also removed all erroneous instances of "gene-", "rna-", and "%2C" from the BED file. These updated files, along with contents.txt, .htaccess, species.txt, and synonyms.txt, have been zipped and re-uploaded as D_Dama.zip on Google Drive.

• rna- and gene- have been removed
• HEADER.md looks good
• species.txt and contents.txt look good

Paige Kulzer - I vote we replace %2C with commas instead of removing them entirely. Without the comma it sounds like one long sentence for some of the descriptions.

Sure thing! I've marked that in the documentation for myself and have made that change in the BED file. The new zip file is up on Google Drive.

Looks good, ready for pull request.

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

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.

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.

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