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statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues
GNU General Public License v3.0
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Papaya genome #476

Open mestato opened 5 years ago

mestato commented 5 years ago

Publication and Data Information

https://www.nature.com/articles/nature06856

This is quite old, lets check around for any newer versions (phytozome, ncbi).

Additional Information

Checklist

See New Genome Documentation for detailed instructions.

RaymondS1 commented 5 years ago

SwissProt

#PBS -N swissprot_blast
#PBS -S /bin/bash
#PBS -j oe
#PBS -A ACF-UTK0011
#PBS -t 1-400
#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/Pawpaw/splits/carica_papaya_cds.fasta.$PBS_ARRAYID \
 -db /lustre/haven/gamma/staton/library/uniprot/uniprot_sprot.fasta \
 -out /lustre/haven/gamma/staton/projects/undergrads/Pawpaw/blast/swissprot/carica_papaya_sprot_$PBS_ARRAYID.xml \
 -evalue 1e-5 \
 -outfmt 5

Trembl

#PBS -N trembl_blast
#PBS -S /bin/bash
#PBS -j oe
#PBS -A ACF-UTK0011
#PBS -t 1-201-400
#PBS -l nodes=1:ppn=2
#PBS -l walltime=10:00:00

cd $PBS_O_WORKDIR

module load blast

blastx \
 -query /lustre/haven/gamma/staton/projects/undergrads/Pawpaw/splits/carica_papaya_cds.fasta.$PBS_ARRAYID \
 -db /lustre/haven/gamma/staton/library/uniprot/uniprot_trembl_plants_July_2018.fasta \
 -out /lustre/haven/gamma/staton/projects/undergrads/Pawpaw/blast/trembl/carica_papaya_trembl_$PBS_ARRAYID.xml \
 -evalue 1e-5 \
 -outfmt 5
RaymondS1 commented 5 years ago

https://hardwoods.ag.utk.edu/organism/Carica/papaya Link to organism

https://hardwoods.ag.utk.edu/Publication/2803342?tripal_pane=gp_sio__references59886 Link to Publication

***https://hardwoods.ag.utk.edu/Genome-assembly/2803343 Reference Genome

https://hardwoods.ag.utk.edu/BLAST-annotation/2803344 SwissProt Annotation

https://hardwoods.ag.utk.edu/BLAST-annotation/2803346 Trembl Annotation

https://hardwoods.ag.utk.edu/InterProScan-annotation/2803347 InterProScan Annotation

https://hardwoods.ag.utk.edu/KEGGresults/2803348 KEGG Annotation

RaymondS1 commented 5 years ago

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/505894 CDS upload

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/505965 Polypeptide Upload

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/505966 RNA published

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/506407 SwissProt Upload

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/506408 Trembl Upload

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/506412 Kegg Upload

https://hardwoods.ag.utk.edu/admin/tripal/tripal_jobs/view/506523 IPS upload

https://hardwoods.ag.utk.edu/content/carica-papaya CDS bdb

https://hardwoods.ag.utk.edu/content/carica-papaya-peptides Peptides bdb

RaymondS1 commented 5 years ago

IPS

#PBS -N carica_papaya_ips
#PBS -A ACF-UTK0011
#PBS -S /bin/bash
#PBS -t 1-200
#PBS -j oe
#PBS -l nodes=1:ppn=4
#PBS -l walltime=10:00:00

cd $PBS_O_WORKDIR

/lustre/haven/gamma/staton/software/interproscan-5.28-67.0/interproscan.sh \
 -i /lustre/haven/gamma/staton/projects/undergrads/pawpaw/ips_splits/carica_papaya_protein.clean.fasta.$PBS_ARRAYID \
 -f XML \
 -d /lustre/haven/gamma/staton/projects/undergrads/pawpaw/IPS/xml \
 --disable-precalc \
 --iprlookup \
 --goterms \
 --pathways \
 --tempdir /lustre/haven/gamma/staton/projects/undergrads/pawpaw/IPS/TMP \
> /lustre/haven/gamma/staton/projects/undergrads/pawpaw/IPS/TMP/$PBS_ARRAYID.out
RaymondS1 commented 5 years ago

https://hardwoods.ag.utk.edu/feature/XP_021886863.1?tripal_pane=group_homology A Feature

RaymondS1 commented 5 years ago

Live Site

https://hardwoodgenomics.org/organism/Carica/papaya Organism

https://hardwoodgenomics.org/Publication/2702051 Publication

https://hardwoodgenomics.org/Genome-assembly/2702052 Reference Genome

https://hardwoodgenomics.org/BLAST-annotation/2702053 Swissprot Annotation

https://hardwoodgenomics.org/BLAST-annotation/2702054 Trembl Annotation

https://hardwoodgenomics.org/InterProScan-annotation/2702055 InterProScan Annotation

https://hardwoodgenomics.org/KEGGresults/2702056 Kegg Annotation

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/655131 CDS Fasta upload

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/662627 Protein Upload

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/662635 RNA published

RaymondS1 commented 5 years ago

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/662654 SwissProt upload

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/662658 Trembl upload

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/662659 IPS upload

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/662660 Kegg upload

https://hardwoodgenomics.org/content/carica-papaya blast database cds

https://hardwoodgenomics.org/content/carica-papaya-peptides blast database peptide

https://hardwoodgenomics.org/feature/XP_021889002.1?tripal_pane=group_homology A Feature

patricksis commented 5 years ago

Jbrowse seems to not look right. It look like it might be a problem of the gff file because I don't see any annotations. @almasaeed2010 https://www.hardwoodgenomics.org/admin/tripal/extension/tripal_jbrowse/management/instances/5

almasaeed2010 commented 5 years ago

I don't see anything wrong with this @patricksis

almasaeed2010 commented 5 years ago

You might just need to clear your browser's cache

patricksis commented 5 years ago

@RaymondS1 This organism looks good, Casey and I have been adding cross references to the organism page and you might want to create download links for the gff file and genome file, but otherwise everything looks good.