Mangrove genome

[mestato]

Publication and Data Information

https://www.nature.com/articles/s41438-020-0300-x

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

[CaseyRichards92]

Download data located here https://bigd.big.ac.cn/gwh/Assembly/990/show

[CaseyRichards92]

Organism created https://hardwoodgenomics.org/organism/Kandelia/Obovata

Needs cross reference associated.

National Genomics Data Center https://bigd.big.ac.cn/ is not an option to select for cross reference on the organism page https://hardwoodgenomics.org/bio_data/add/1
@almasaeed2010 or @noahcaldwell7 could you help with adding this option?

Publication needs this as well https://hardwoodgenomics.org/bio_data/add/5

[CaseyRichards92]

Publication created https://hardwoodgenomics.org/Publication/3959609?tripal_pane=group_summary_tripalpane

[CaseyRichards92]

Reference genome created https://hardwoodgenomics.org/Genome-assembly/3959610?tripal_pane=group_summary_tripalpane

• Needs downloads

[CaseyRichards92]

IPS Annotation https://hardwoodgenomics.org/InterProScan-annotation/3959611
Swissprot annotation https://hardwoodgenomics.org/BLAST-annotation/3959612
Tremble annotation https://hardwoodgenomics.org/BLAST-annotation/3959613
KEGG Annotation https://hardwoodgenomics.org/KEGGresults/3959615

[CaseyRichards92]

FASTA Loader peptides https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/876391

[CaseyRichards92]

FASTA Loader CDS https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877040

[CaseyRichards92]

Published peptides job https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877041

[CaseyRichards92]

TrEMBL Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877059
Swissprot Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877060

[CaseyRichards92]

JBROWSE Track https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877062
JBROWSE Instance https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877061

[CaseyRichards92]

Blast DB CDS https://hardwoodgenomics.org/content/kandelia-obovata-transcripts
Blast DB PEP https://hardwoodgenomics.org/content/kandelia-obovata-peptides
Blast DB Scaffolds https://hardwoodgenomics.org/content/kandelia-obovata-scaffolds

[CaseyRichards92]

KEGG Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877066

[CaseyRichards92]

JBrowse Link created https://hardwoodgenomics.org/tools/jbrowse/?data=data%2Fkandelia_obovata__mangrove%2Fdata&tracks=mangrove%2CDNA&loc=GWHACBH00000001%3A1..13452090&highlight=

[CaseyRichards92]

IPS Loader https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/877100

[CaseyRichards92]

@almasaeed2010 @noahcaldwell7 I am receiving this error when trying to save the downloads in the description box.

Could not save the TripalEntity: SQLSTATE[42703]: Undefined column: 7 ERROR: column "organism_id" of relation "analysis" does not exist LINE 1: ...= NULL, sourceuri = NULL, analysis_id = '384', organism_i... ^
Cannot save entity

https://hardwoodgenomics.org/Genome-assembly/3959610?tripal_pane=group_downloads
HTML trying to load

<h4>Downloads</h4>
<table class="table table-valign-middle table-sm table-hover">
	<tbody>
		<tr class="no-border">
		<td class="text-muted download-td"><i class="fa fa-file-text-o"></i></td>
		<th>
			Genomic scaffolds
			<div>
				<a class="text-sm text-muted font-normal" href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.genome.fasta">Genomic scaffolds</a>
			</div>
		</th>
		<td class="text-right"><a href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.genome.fasta" class="btn btn-primary"><i class="fa fa-download"></i></a></td>
		</tr>
		<tr class="no-border">
		<td class="text-muted download-td"><i class="fa fa-file-text-o"></i></td>
		<th>
			All Gene Models CDS
			<div>
				<a class="text-sm text-muted font-normal" href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.RNA.fasta">All Gene Models CDS</a>
			</div>
		</th>
		<td class="text-right"><a href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.RNA.fasta" class="btn btn-primary"><i class="fa fa-download"></i></a></td>
		</tr>
		<tr class="no-border">
		<td class="text-muted download-td"><i class="fa fa-file-text-o"></i></td>
		<th>
			All Gene Models Protein
			<div>
				<a class="text-sm text-muted font-normal" href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.Protein.faa">All Gene Models Protein</a>
			</div>
		</th>
		<td class="text-right"><a href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.Protein.faa" class="btn btn-primary"><i class="fa fa-download"></i></a></td>
		</tr>
		<tr class="no-border">
		<td class="text-muted download-td"><i class="fa fa-file-text-o"></i></td>
		<th>
			All Gene Models GFF
			<div>
				<a class="text-sm text-muted font-normal" href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.gff">All Gene Models GFF</a>
			</div>
		</th>
		<td class="text-right"><a href="/sites/default/files/sequences/kandelia_obovata/GWHACBH00000000.gff" class="btn btn-primary"><i class="fa fa-download"></i></a></td>
		</tr>
	</tbody>
</table>

[almasaeed2010]

@cricha59 this issue has been resolved by @jwest60 and @noahcaldwell7 so you should now never encounter this issue again 😃

[CaseyRichards92]

Looks good! https://hardwoodgenomics.org/Genome-assembly/3959610?tripal_pane=group_downloads Thanks @jwest60 @almasaeed2010 @noahcaldwell7