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:2
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Epic Link:
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Sprint:Fall 1, Fall 7
Description
Task: Add the Hydra vulgaris genome and annotation to IGB. Current Hydra vulgaris genome version provided by ensembl: Hydra_105_v3 (Feb 2022).
Hydra vulgaris (HydraT2T_AEP)(Apr 2024) - https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_038396675.1/
Attachments
Activity
I have deployed the latest copy of quickload repository to:
RENCI hosting - http://igbquickload-main.bioviz.org/quickload/ (primary)
UNC Charlotte hosting - http://igbquickload.org/quickload/ (backup)
To test:
- launch IGB and visit each new genome version (see above)
- visit the subdirectories for each genome (by following the links above) and check that there is text describing the genome and datasets visible in IGB itself
- within IGB Available Data section, click any "linkout" icons and make sure a Web page opens and that it goes to a place that describes the dataset somehow
- check that when the datasets load, they look OK - gene models should be boxes with lines connecting them, for instance, and the track labels should be readable and should make sense ("making sense" is a subjective of course! mainly we're looking for problems that could trip up a user and cause confusion.)
The SVN site is back up and running, and the Hydra vulgaris genome has been pushed to the SVN repo.
Ready for final review!
The subversion repository appears to be down which is preventing me from pushing this quickload to the SVN site. When I try to check-in my changes, svn is responding with
svn: E200029: Commit failed (details follow): svn: E200029: could not begin a transaction
And when I try to update my working copy with "svn update", svn is responding with
svn: E200029: Couldn't perform atomic initialization
Ann Loraine, could you restart the svn site and reattach the virtual hard drive storing the data like you did for IGBF-3748?
Testing: everything looks good.
Below is an outline of the steps I followed to create the Hydra vulgaris Quickload:
1. Convert genome .fna to .2bit
gunzip GCF_038396675.1_HydraT2T_AEP_genomic.fna.gz ./faToTwoBit GCF_038396675.1_HydraT2T_AEP_genomic.fna H_vulgaris_Apr_2024.2bit
2. Create genome.txt
./twoBitInfo H_vulgaris_Apr_2024.2bit genome.txt
3. Get gene models from NCBI (.gff), then convert .gff to .bed
cd ~/Documents/Repos/genomesource ./gff3ToBedDetail.py -g ~/Downloads/genomic.gff -b ~/Downloads/H_vulgaris_Apr_2024_refGene.bed
4. Check if UCSC has any information for this genome using its txid (NCBI:txid6087) and, since if it does, compare gene names/ID's to those present in the .bed file created in the previous step
cd ~/Downloads gunzip -c gene2accession.gz | grep '^6087\t' > 6087.gene2accession.txt
5. Sort, gzip, and tabix the .bed file
sort -k1,1 -k2,2n H_vulgaris_Apr_2024_refGene.bed | bgzip > H_vulgaris_Apr_2024_refGene.bed.gz tabix -0 -s 1 -b 2 -e 3 H_vulgaris_Apr_2024_refGene.bed.gz
6. 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.
7. Create annots.xml and add _H_vulgaris_ to contents.txt and .htaccess
cd ~/Documents/Repos/quickload svn mkdir H_vulgaris_Apr_2024 svn cp A_gambiae_Oct_2006/annots.xml H_vulgaris_Apr_2024 nano H_vulgaris_Apr_2024/annots.xml nano contents.txt nano .htaccess
Tested following instructions above. Everything looks good.
Closing ticket.