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Genome assembly update: Heliothis virescens #271

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9 of 20 tasks
amcooksey opened this issue Feb 27, 2024 · 7 comments
Open
9 of 20 tasks

Genome assembly update: Heliothis virescens #271

amcooksey opened this issue Feb 27, 2024 · 7 comments
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@mpoelchau
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@amcooksey
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amcooksey commented Feb 27, 2024 •
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OGS remapping

  • request whole-genome alignment
  • Set up data directories and get data
  • run remap-gff3

manual annotation remapping

  • request whole-genome alignment
  • Set up data directories and get data
  • run remap-gff3

Change old content

  • back up and deprecate old Apollo2
  • back up and deprecate old fasta files in BLAST
  • back up and deprecate old fasta files in Hmmer

Add new content to i5k Workspace applications

See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)

  • assembly accession number: GCA_002382865.2
  • publication associated with assembly: TBD
  • due date: 3/27
  • community contact: Megan Fritz, [email protected]

Tasks on Ceres:

Tasks on the NAL servers:
@amcooksey amcooksey self-assigned this Feb 27, 2024
@mpoelchau
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Let's put this one at the back of the queue - I should check in with Megan on her group's annotation status first.

@amcooksey
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OGS, manual annotations and RNAseq all loaded into apollo. waiting for space on i5k to finish the update.

@amcooksey
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I think this is completely updated now. I was only able to obsolete the old assembly on production. The stage admin menu doesn't have all of the same options as production.

@MonicaPoelchau-USDA
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@amcooksey What was missing on stage?

@amcooksey
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production:
image

stage:
image

@MonicaPoelchau-USDA
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  • Looks like there's a publication associated with the genome assembly - can you add this? https://doi.org/10.1016/j.ygeno.2022.110441
  • I changed the method from liftover to LiftOff in the OGS tripal page
  • Can you add text about the update in the organism page description?
  • Were there unmapped features? If so, we should include the unmapped_features.txt file in the data downloads. Otherwise we need to state in the readme that all features mapped.
  • I will update the OGS description
  • I will set up the OGS Ag Data Commons submission

@amcooksey
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I added publication, updated the org page description and added the unmapped_features.txt file

@mpoelchau mpoelchau assigned mpoelchau and unassigned amcooksey Nov 13, 2024
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