Juglans regia v 2.0 - Githubissues

statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues

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Juglans regia v 2.0 #596

Open MattHuff opened 4 years ago

MattHuff commented 4 years ago

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.

[x] Create Organism
[x] Create Publication
[x] Create Reference Genome
[x] Create InterProScan Annotation
[x] Create BLAST Annotation
[x] Run Chado FASTA Loader for CDS
[x] Run Chado FASTA Loader for Polypeptides
[x] Publish Tripal content
[x] Create KEGG Annotation
[x] Run Chado KEGG Loader
[x] Run Chado BLAST XML results loader
[x] Run Chado InterProScan XML results loader
[x] Create Blast Database

CaseyRichards92 commented 4 years ago

Running blast, trembl, and ips on ACF

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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

CaseyRichards92 commented 4 years ago

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