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Vitis vinifera Genome Upload #600

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MattHuff opened this issue Aug 3, 2020 · 13 comments
Open
13 tasks done

Vitis vinifera Genome Upload #600

MattHuff opened this issue Aug 3, 2020 · 13 comments
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@patricksis @CaseyRichards92 @RaymondS1
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data upload Load into Chado Undergraduate Task

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@MattHuff
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MattHuff commented Aug 3, 2020 •
edited by CaseyRichards92
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Publication and Data Information

https://www.nature.com/articles/nature06148

Additional Information

This information can be accessed through Phytozome; you will need an account with JGI to download these files. We want the versions listed under "v2.1".

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
@CaseyRichards92
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Running BLAST and IPS

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Organism created https://hardwoodgenomics.org/organism/Vitis/vinifera?tripal_pane=group_summary_tripalpane

@CaseyRichards92
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Reference genome https://hardwoodgenomics.org/Genome-assembly/4228758?tripal_pane=group_summary_tripalpane

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CDS Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903341
Peptides Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903342
Published peptides https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903343

@CaseyRichards92
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Swissprot Annotation - https://hardwoodgenomics.org/BLAST-annotation/4228759
Trembl Annotation - https://hardwoodgenomics.org/BLAST-annotation/4228760

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Swissprot loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903347

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TREMBL Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903348

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IPS Annotation https://hardwoodgenomics.org/InterProScan-annotation/4240624

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KEGG Annotation https://hardwoodgenomics.org/KEGGresults/4243528

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Gene Atlas https://hardwoodgenomics.org/Gene-expression-profiling/4244032

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IPS Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903655
KEGG Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903659

@CaseyRichards92
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JBrowse https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/903661

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BLAST DB Transcripts https://hardwoodgenomics.org/content/vitis-vinifera-transcripts
BLAST DB Peptides https://hardwoodgenomics.org/content/vitis-vinifera-peptides
BLAST DB Scaffolds https://hardwoodgenomics.org/content/vitis-vinifera-scaffolds

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@CaseyRichards92 CaseyRichards92

@RaymondS1 RaymondS1

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@MattHuff @patricksis @CaseyRichards92 @RaymondS1