New Quercus lobata genome version - Githubissues

statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues

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New Quercus lobata genome version #536

Open mestato opened 4 years ago

mestato commented 4 years ago

Publication and Data Information

Data:

Additional Information

Need to have downloads for Versions 0.5, 1.0, 2.0 and 3.0. Need to update genome features to the new ones from v3.0. (Delete old ones).

I can currently only find the new v3.0 annotation as a GenBank file. I believe Jiali has some files that she got from the authors, ask her, and also look around for gff and fasta files. If that doesn't work, we'll convert from genbank to the needed file types.

Checklist

See New Genome Documentation for detailed instructions.

[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

patricksis commented 4 years ago

CDS fasta loader: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/841480 peptide fasta loader: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/841481

patricksis commented 4 years ago

Reference genome page is updated with 3.0 downloads

patricksis commented 4 years ago

Swissprot annotation: https://www.hardwoodgenomics.org/BLAST-annotation/3890873 trembl annotation: https://www.hardwoodgenomics.org/BLAST-annotation/3890874 IPS annotation: https://www.hardwoodgenomics.org/InterProScan-annotation/3890875 Published tripal content: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/842226 trembl xml upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/846550 swissprot xml upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/846554 IPS xml upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/846558

patricksis commented 4 years ago

KEGG annotation: https://www.hardwoodgenomics.org/KEGGresults/3930250 KEGG loader: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/847279

patricksis commented 4 years ago

bdb transcripts: https://www.hardwoodgenomics.org/content/quercus-lobata-transcripts Peptides: https://www.hardwoodgenomics.org/content/quercus-lobata-peptides