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Malus domestica Reference Genome #590

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patricksis opened this issue May 28, 2020 · 3 comments
Open
13 tasks done

Malus domestica Reference Genome #590

patricksis opened this issue May 28, 2020 · 3 comments
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@patricksis

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@patricksis
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patricksis commented May 28, 2020 •
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Publication and Data Information

https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Mdomestica

Additional Information

Checklist

See New Genome Documentation for detailed instructions.

  • Create Organism
  • Create Publication
  • Create Reference Genome
  • Create InterProScan Annotation
  • Create BLAST Annotation
  • Run Chado FASTA Loader for CDS
  • Run Chado FASTA Loader for Polypeptides
  • Publish Tripal content
  • Create KEGG Annotation
  • Run Chado KEGG Loader
  • Run Chado BLAST XML results loader
  • Run Chado InterProScan XML results loader
  • Create Blast Database
@patricksis patricksis self-assigned this May 29, 2020
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patricksis commented May 29, 2020 •
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Organism:
https://hardwoodgenomics.org/organism/Malus/domestica?tripal_pane=group_summary_tripalpane
Publication:
https://hardwoodgenomics.org/Publication/4073221
Reference Genome:
https://hardwoodgenomics.org/Genome-assembly/4073223?
IPS annotation:
https://hardwoodgenomics.org/InterProScan-annotation/4073224
Swissprot annotation:
https://hardwoodgenomics.org/BLAST-annotation/4073225
Trembl annotation:
https://hardwoodgenomics.org/BLAST-annotation/4073226
CDS loader:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/882290
Polypeptide loader:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/882294
Published tripal content:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/882523
Trembl xml loader:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/887708
Swissprot xml loader:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/887715
IPS xml loader:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/887738
KEGG annotation:
https://hardwoodgenomics.org/KEGGresults/4148737
KEGG loader:
https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/888355

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transcripts bdb:
https://hardwoodgenomics.org/content/malus-domestica-transcripts
peptides bdb:
https://hardwoodgenomics.org/content/malus-domestica-peptides
scaffolds bdb:
https://hardwoodgenomics.org/content/malus-domestica-scaffolds

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Jbrowse:
https://hardwoodgenomics.org/admin/tripal/extension/tripal_jbrowse/management/instances/34

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