Request assembly
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Mi Cheong Cheong
Mar 24, 2021, 6:25:47 PM3/24/21
to gen...@soe.ucsc.edu
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Hello,
-
I am Mi Cheong Cheong from UTSW. I cannot find the assembly for Strongyloides stercoralis.
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Can you add Strongyloides stercoralis assembly?
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- GenBank assembly accession:
- GCA_000947215.1 (latest)
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- Thank you,
- Mi Cheong Cheong
|
UT Southwestern |
|
Medical Center |
|
The future of medicine, today. |
Brian Lee
Mar 24, 2021, 7:59:46 PM3/24/21
to Mi Cheong Cheong, gen...@soe.ucsc.edu
Dear Cheong,
Thank you for using the UCSC Genome Browser and your suggestion for adding the Strongyloides stercoralis assembly (GCA_000947215.1).
Your request is very helpful for aiding us in prioritizing our work knowing what new assemblies would be of use and of interest to our users. We have methods of automatically generating the files from Genbank to allow the attachment of assemblies to the UCSC Genome Browser, such as http://genome.ucsc.edu/h/GCF_001040885.1 which will load the Strongyloides ratti (nematodes) assembly (Genbank = GCA_001040885.1 / RefSeq = GCF_001040885.1).
In time if a GCF_ RefSeq accession is made and an assembly hub is built for Strongyloides stercoralis a URL such as https://genome.ucsc.edu/h/GCF_proper_accession would work (it will not work until the files have been created and placed on a server).
One other option is to make an assembly hub independently and to host the data on your servers. This allows researchers to take complete control over the version of the data and the annotation files. See more about Assembly Hubs here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly
Also, you may consider connecting with the developers of the WormBase Public Hub (he...@wormbase.org), they have built assembly hubs (and have one for Strongyloides ratti) and might add one for Strongyloides stercoralis.
Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
Thank you for using the UCSC Genome Browser and your suggestion for adding the Strongyloides stercoralis assembly (GCA_000947215.1).
Your request is very helpful for aiding us in prioritizing our work knowing what new assemblies would be of use and of interest to our users. We have methods of automatically generating the files from Genbank to allow the attachment of assemblies to the UCSC Genome Browser, such as http://genome.ucsc.edu/h/GCF_001040885.1 which will load the Strongyloides ratti (nematodes) assembly (Genbank = GCA_001040885.1 / RefSeq = GCF_001040885.1).
In time if a GCF_ RefSeq accession is made and an assembly hub is built for Strongyloides stercoralis a URL such as https://genome.ucsc.edu/h/GCF_proper_accession would work (it will not work until the files have been created and placed on a server).
One other option is to make an assembly hub independently and to host the data on your servers. This allows researchers to take complete control over the version of the data and the annotation files. See more about Assembly Hubs here: http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Assembly
Also, you may consider connecting with the developers of the WormBase Public Hub (he...@wormbase.org), they have built assembly hubs (and have one for Strongyloides ratti) and might add one for Strongyloides stercoralis.
Thank you again for your inquiry and for using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.
All the best,
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