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Juglans regia v 2.0 #596

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MattHuff opened this issue Jul 20, 2020 · 10 comments
Open
13 tasks done

Juglans regia v 2.0 #596

MattHuff opened this issue Jul 20, 2020 · 10 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 Jul 20, 2020 •
edited by CaseyRichards92
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Publication and Data Information

https://academic.oup.com/gigascience/article/9/5/giaa050/5841058

Additional Information

We have been using the J. regia_ 2.0 genome for the tree gene atlas project. However, the 2.0 genes have not yet been loaded onto the website, which is causing issues for the phylotrees - as it is looking for genes that do not exist - and will cause issues if we load the TPM counts. Before loading the counts data, please be sure to load the BLAST/IPS results.

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, trembl, and ips on ACF

@CaseyRichards92
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CDS Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/898140

@CaseyRichards92
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Peptides loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/898141

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Published peptides https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/898142

@CaseyRichards92
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New swissprot annotation https://hardwoodgenomics.org/BLAST-annotation/4209957

@CaseyRichards92
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Swissprot loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/898272

@CaseyRichards92
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New IPS Annotation https://hardwoodgenomics.org/InterProScan-annotation/4210010
IPS Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899254

@CaseyRichards92
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KEGG Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899306

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Trembl Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/899364

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BLAST DB Transcripts https://hardwoodgenomics.org/content/juglans-regia-genome-transcripts
BLAST DB Proteins https://hardwoodgenomics.org/content/juglans-regia-genome-peptides
BLAST DB Scaffolds https://hardwoodgenomics.org/content/juglans-regia-genome-scaffolds

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@CaseyRichards92 CaseyRichards92

@RaymondS1 RaymondS1

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@MattHuff @patricksis @CaseyRichards92 @RaymondS1