Mulberry genome

[mestato]

Original paper: https://www.nature.com/articles/ncomms3445

DB: https://morus.swu.edu.cn/

[almasaeed2010]

Downloadables can be found here: https://morus.swu.edu.cn/morusdb/datasets

[patricksis]

Organism upload: https://hardwoods.ag.utk.edu/organism/Morus/notabilis

[patricksis]

Genome assembly: https://hardwoods.ag.utk.edu/Genome-assembly/2360507

[patricksis]

cds upload job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/696233

[patricksis]

protein upload job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/700014 regular expression used: >(.*?) t protein job re-upload: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/700024 same reg expression used

[patricksis]

acf blast analysis:

#PBS -N swissprot_BLAST
#PBS -S /bin/bash
#PBS -j oe
#PBS -A ACF-UTK0011
#PBS -t 1-200
#PBS -l nodes=1:ppn=2
#PBS -l walltime=04:00:00

cd $PBS_O_WORKDIR

module load blast

blastx \
 -query /lustre/haven/gamma/staton/projects/undergrads/mulberry/raw_data/BLAST-split/morus_notabilis.cds.fast$
 -db /lustre/haven/gamma/staton/library/uniprot/uniprot_sprot.fasta \
 -out /lustre/haven/gamma/staton/projects/undergrads/mulberry/BLAST/swissprot/mulberry_swissprot_$PBS_ARRAYID$
 -evalue 1e-5 \
 -outfmt 5

[patricksis]

Trembl job on acf

#PBS -S /bin/bash
#PBS -j oe
#PBS -A ACF-UTK0011
#PBS -t 1-200
#PBS -l nodes=1:ppn=2
#PBS -l walltime=07:00:00

cd $PBS_O_WORKDIR

module load blast

blastx \
 -query /lustre/haven/gamma/staton/projects/undergrads/mulberry/raw_data/BLAST-split/morus_notabilis.cds.fast$
 -db /lustre/haven/gamma/staton/libraries/uniprot/uniprot_trembl_plants_July_2018.fasta \
 -out /lustre/haven/gamma/staton/projects/undergrads/mulberry/BLAST/trembl/mulberry_trembl_$PBS_ARRAYID$
 -evalue 1e-5 \
 -outfmt 5

[patricksis]

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/710261 Job page for InterPro scan

[patricksis]

Publish Gene Job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/714578

[patricksis]

Blastx Annotation (trembl): https://hardwoods.ag.utk.edu/Analysis/2445478 Blastx Annotation (Swissprot): https://hardwoods.ag.utk.edu/BLAST-annotation/2445479 Organism page: https://hardwoods.ag.utk.edu/organism/Morus/notabilis Genome assembly: https://hardwoods.ag.utk.edu/Genome-assembly/2360507 InterProScan Annotation: https://hardwoods.ag.utk.edu/InterProScan-annotation/2418511 Publication: https://hardwoods.ag.utk.edu/Publication/2525405

[patricksis]

Trembl import job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/718534

[patricksis]

SwissProt import job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/728752

[patricksis]

Morus notabilis - BLASTx Annotation(SwissProt): https://hardwoods.ag.utk.edu/BLAST-annotation/2445479

[patricksis]

Fixed trembl import job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/728967 reg expression used: (L.*.t\d\d)

[patricksis]

fixed swissprot import job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/728972 reg expression used: (L.*.t\d\d)

[patricksis]

interProScan import job: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/730803

[mestato]

For the organism page, I made the links to the sources clickable. For the reference genome description, could you add links to download the files (fasta, gff, etc) and the publication associated with the analysis.

[patricksis]

will do

[almasaeed2010]

@patricksis Everything looks good except for the publication. It's created but nor linked to the genome assembly. You need to edit the assembly and choose it under publications.

[mestato]

Updated ref genome analysis description to fix links.

[patricksis]

Main site Organism page: https://www.hardwoodgenomics.org/organism/Morus/notabilis Reference Genome: https://www.hardwoodgenomics.org/Genome-assembly/2335717 Publication: https://www.hardwoodgenomics.org/Publication/2335718 InterProScan Annotation: https://www.hardwoodgenomics.org/InterProScan-annotation/2335719 Trembl Annotation: https://www.hardwoodgenomics.org/BLAST-annotation/2335720 Swissprot Annotation: https://www.hardwoodgenomics.org/BLAST-annotation/2335721

[patricksis]

cds upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/469971 protein upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/469975

[patricksis]

Uploaded split protein file to blastKOALA. Pearl script used: perl /lustre/haven/gamma/staton/unpublished_lab_code/perl/fasta_scripts/split.pl morus_notabilis.protein.fasta 6

[patricksis]

IPS job (Live) https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/501451

[patricksis]

MRNA publishing job; https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/476534

[patricksis]

Live site swissprot upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/501406

[patricksis]

live site trembl upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/501388

[patricksis]

KEGG annotation: https://hardwoodgenomics.org/KEGGresults/2509829 KEGG job: https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/516855

[patricksis]

WD trp_kegg: ERROR: Unable to find KEGG term: 'K22943' [warning] @bradfordcondon is this an issue that needs to be addressed when uploading KEGG?

[bradfordcondon]

ugh yeah that is a problem on the back end not your end. 1 second

[bradfordcondon]

Short answer: that term was added to kegg after the OBO was built... solutions:

• insert it manually
• delete it from the annotation file
• wait for the issue to get fixed in the module so that we can regenerate and re-load the OBO properly.

see #456 for issue discussion.

[patricksis]

Dev site: BLAST db for cds: https://hardwoods.ag.utk.edu/content/morus-notabilis-transcripts For peptides: https://hardwoods.ag.utk.edu/content/morus-notabilis-peptides

[patricksis]

Live site: BLAST DB for cds https://www.hardwoodgenomics.org/content/morus-notabilis-transcripts For peptides: https://www.hardwoodgenomics.org/content/morus-notabilis-peptides

[almasaeed2010]

Looks like the polypeptides were loaded incorrectly in that it was indicated that this polypeptide is "part of" the mrna instead of "derived from." Therefore, we need to reload the peptides but the good news is that we don't have to reload anything else. @patricksis please talk to me about this when you are here.

select * from chado.feature_relationship where subject_id = '5168696';
 feature_relationship_id | subject_id | object_id | type_id | value | rank 
-------------------------+------------+-----------+---------+-------+------
                 2314871 |    5168696 |   5141731 |      73 |       |    0

Note that the subject and object are flipped (5141731 should be the subject).

[patricksis]

Peptides re-upload: https://www.hardwoodgenomics.org/admin/tripal/tripal_jobs/view/719162

[mestato]

Looks like the gff is available through ncbi (https://www.ncbi.nlm.nih.gov/genome/?term=txid981085[Organism:noexp]). @patricksis could you grab it and add to downloads and use for JBrowse?

[patricksis]

JBrowse instance: https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/548611

[patricksis]

Jbrowse instance for live: https://www.hardwoodgenomics.org/admin/tripal/extension/tripal_jbrowse/management/instances/10

[patricksis]

gff track is not showing up here. I don't think the names from the genome and gff match up

[mestato]

@mestato work on fasta and gff files, see server location: /var/www/html/sites/default/files/sequences/mulberry/raw_data

[CaseyRichards92]

@patricksis Here is what this organism needs.

• [x] Cross reference added
• [x] KEGG job didnt work correctly. Issue: Unable to identify the feature for 'L484_001038.p01' https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/516855
• [ ] JBrowse still having issues

[patricksis]

@cricha59 this is a known issue with KEGG, we have an issue #456. KEGG does it for every organism I'm pretty sure.

[patricksis]

Cross references have been added, the only thing left for the organism is to fix JBrowse.