search

statonlab / hardwoods_site

Hardwoods Genomics bugs, data loading, and general issues
GNU General Public License v3.0
2 stars 1 forks source link

Populas deltoides is missing BLAST #468

Closed almasaeed2010 closed 5 years ago

almasaeed2010 commented 5 years ago

https://hardwoodgenomics.org/organism/Populus/deltoides?tripal_pane=group_summary_tripalpane

We need to run BLAST for this organism.

I'll try to find the fasta files for it

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/populus_deltoides/splits2/populus_deltoides_cds.fasta.$PBS_ARRAYID \
 -db /lustre/haven/gamma/staton/library/uniprot/uniprot_sprot.fasta \
 -out /lustre/haven/gamma/staton/projects/undergrads/populus_deltoides/blast/swissprot/juglan_microcarpa_sprot_$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/populus_deltoides/splits/gene_search_result.fasta.$PBS_ARRAYID \
 -db /lustre/haven/gamma/staton/library/uniprot/uniprot_trembl_plants_July_2018.fasta \
 -out /lustre/haven/gamma/staton/projects/undergrads/populus_deltoides/blast/trembl/populus_deltoides_trembl_$PBS_ARRAYID.xml \
 -evalue 1e-5 \
 -outfmt 5
RaymondS1 commented 5 years ago

https://hardwoodgenomics.org/BLAST-annotation/2665697 SwissProt Annotation

https://hardwoodgenomics.org/BLAST-annotation/2665699 Trembl Annotation

RaymondS1 commented 5 years ago

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/620666 SwissProt Upload

https://hardwoodgenomics.org/admin/tripal/tripal_jobs/view/622909 Trembl Upload

RaymondS1 commented 5 years ago

Link to finished organism https://hardwoodgenomics.org/organism/Populus/deltoides

Link to mRNA page https://hardwoodgenomics.org/feature/Podel01G2127001?tripal_pane=group_summary_tripalpane

almasaeed2010 commented 5 years ago

Looks done. Thanks @RaymondS1