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:0.5
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Epic Link:
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Sprint:Spring 1, Spring 2, Spring 3, Spring 4
Description
We are offering a genome assembly for painted lady as part of our Quickload site - see: http://igbquickload-main.bioviz.org/quickload/V_cardui_Feb_2021/
However, the in the HEADER file (see above link) does not have enough information for a user to locate the original files we used to create our IGB-friendly versions of the files. This can become a problem for users who are working with bioinformatics pipelines that use assembly or annotation files. They will need to know if the files we are showing in IGB are the same as the files they are working with, or not.
Also, it would be good to link to a research article describing this assembly, to help users learn more about this assembly.
For this task, improve the documentation so that a user who clicks the "get info" link within IGB will be able to find information needed to locate the original data files we used to create our IGB-friendly versions for the Quickload repository.
Notes:
- It looks like this might be "the" painted lady genome paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC10061037
Attachments
Issue Links
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- Closed
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Activity
Thank you for your patience with my many questions.
How about if I make a stab at updating the documentation?
Then you can see if I got it right or not, and correct as needed?
New documentation page is deployed to IGB quickload sites and ready for testing.
See: https://data.bioviz.org/quickload/D_dama_Nov_2023/
Question for Ann Loraine - Did you forget to link to the research article describing this Dama dama assembly (see https://www.sciencedirect.com/science/article/pii/S2666937423000124#da0005)?
I've added mention of the research article I mentioned in my previous comment. This update has been pushed to the SVN repository which is now at revision 228. This new documentation format is clear, concise, and easy to follow. Ready for a final review by Ann Loraine!
Our quickload sites are now updated to revision 228. New documentation is deployed. I checked all the links and they all go to the expected location.
Moving to Done.
I've added a link to the research article describing this assembly to HEADER.md
. There, direct links to the sequence files (chromosome-specific FASTAs) on ENA are provided in the Data Availability section. The NCBI Genomes resource is also linked in HEADER.md
and the specific genome assembly (ilVanCard2.1) has been specified in the first line so that a user can determine which of the reference genomes we used.
Ready for review, as well as any more suggestions for improving quickload descriptions!