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:
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Story Points:0.5
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Sprint:Fall 2018 1, Fall 2018 Sprint 2, Fall 2018 Sprint 3
Description
A user from HELP-279 has contacted us about the June 2008 S. Cerevisiae genome missing from IGB Quickload.
To aid in the task of adding this genome, I have attached the:
1) 2bit reference genome, obtained here:
http://hgdownload.soe.ucsc.edu/goldenPath/sacCer2/bigZips/
2) Reference Annotations in BED format, obtained from the UCSC Table Browser using the "SGD Gene" track
Attachments
Issue Links
Activity
Deployed as part of current (newly migrated) quickload site.
To test:
- Test using master branch installer for 9.0.2
- Inspect Species menu of Current Genome tab; check for new yeast genome related menu options (IGB has a bug whereby newly added genomes are shown incorrectly using their UCSC-style or other synonyms)
- Select Current Genome tab, select Saccharomyces cerevisiae species (this is budding yeast)
- Check that 2008 genome is listed in genome version menu
- Select 2008 genome
- Make sure that reference gene model data set is loaded upon visiting the genome
- Make sure that sequence data can be loaded
- Make sure that the menu item in Current Genome lists the species and genome correctly, with correct tooltips
Report any problems here and if there are problems, return to To-Do column.
- Added to new https://svn.bioviz.org/repos/genomes subversion repository. To browse, visit https://svn.bioviz.org/viewvc (visit on non-UNCC network due to issues with internal DNS, to be fixed soon)
- However, did not add S_cerevisiae_Jun_2008_refGene.bed.gz because it is not mentioned in the annots.xml file.
This is ready for review.
Remember, you can access the quicklaod site for the 2008 S.Cerevisiae genome assembly here:
http://18.222.191.240/Quickload_IGBF-1189_S.Cerevisiae/
I am assigning this to Ann for review.
Please see my last comment.
If this passes review then Ann can take over.
The gene descriptions were added following the instructions here:
https://wiki.transvar.org/display/igbdevelopers/Updating+RefGene+UCSC+data+set+for+an+existing+genome+in+IGB+QuickLoad
With some modification.
I encountered a problem with the ucscToBedDetail.py script from the GenomeSource repo:
https://bitbucket.org/lorainelab/genomesource
That issue has been resolved.
The authoritative body for this genome is SDG. UCSC provides a bed table of sdg genes. The identifiers used in this bed file are locus_ids, which is an available field in the gene_info file from ncbi. I modified the ucscToBedDetail.py script to filter by taxID and use the locus id rather than the gene id to get the information from the gene_info table. I copied the modified script (ucscToBedDetail_SacCer_locusID.py) to the test quickload site so Ann and include it as documentation if appropriate.
Out of 6,717 models in the sdg genes bed file, 698 were not found in the gene_info list (so they have NA for the gene description).
Create and test Quickload containing just these data and notify Dr. Loraine when it is ready to deploy.
Ensure appropriate synonyms are added to synonyms.txt and species.txt bundled with IGB.
Tested as described, the application behaves as expected.