New organism (Apollo and gw only): Culex quinquefasciatus

[mpoelchau]

See https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update for full description of each task (requires gitlab login)

• assembly accession number: GCF_015732765.1

• publication associated with assembly: Not published, please follow Ft. Lauderdale/Toronto guidelines for data re-use

• [x] @ShangYuChiang 1. Run the final_workflow.cwl component of the organism_onboarding pipeline. https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-an-organism-CWL-update#1-run-the-final_workflowcwl-component-of-the-organism_onboarding-pipeline-httpsgithubcomnal-i5korganism_onboarding

  • [x] @ShangYuChiang 2. Add RNA-Seq. https://gitlab.com/i5k_Workspace/workspace_roadmap/-/wikis/Adding-RNA-Seq-data-to-an-i5k-Workspace-project-with-the-NAL_RNA_seq_annotation_pipeline

Monica will finish this one up (i think).

[mpoelchau]

genomics-workspace commands:

sudo su -l i5k
#1. Copy fasta files
cp /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/scaffold/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna /usr/local/i5k/media/blast/db/
cp /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/scaffold/analyses/Culex_quinquefasciatus_Annotation_Release_100/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_cds_from_genomic.fna /usr/local/i5k/media/blast/db/
cp /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/scaffold/analyses/Culex_quinquefasciatus_Annotation_Release_100/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_rna_from_genomic.fna /usr/local/i5k/media/blast/db/
cp /app/data/other_species/culqui/VPISU_Cqui_1.0_pri_paternal/scaffold/analyses/Culex_quinquefasciatus_Annotation_Release_100/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa /usr/local/i5k/media/blast/db/

2. add info to app

python manage.py addorganism Culex quinquefasciatus

#genome fasta: 
python manage.py addblast Culex quinquefasciatus  -t nucleotide Genome Assembly -f GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna -d 'Culex quinquefasciatus genome assembly, ASM1558622v1'

#RNA fasta file: 
python manage.py addblast Culex quinquefasciatus -t nucleotide Transcript -f GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_rna_from_genomic.fna -d 'Culex quinquefasciatus NCBI Annotation release 100, transcripts'

#Peptide fasta file: 
python manage.py addblast Culex quinquefasciatus -t peptide Protein -f GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa -d 'Culex quinquefasciatus NCBI Annotation release 100, translated CDS'

#CDS fasta file: 
python manage.py addblast Culex quinquefasciatus -t nucleotide Transcript -f GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_cds_from_genomic.fna -d Culex quinquefasciatus NCBI Annotation release 100, CDS

#Process each fasta file:

#genome fasta: 
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna  -m
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna  -p
python  manage.py  blast_shown  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna  --shown true

#RNA fasta file: 
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_rna_from_genomic.fna  -m
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_rna_from_genomic.fna  -p
python  manage.py  blast_shown  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_rna_from_genomic.fna  --shown true

#Peptide fasta file: 
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa  -m
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa  -p
python  manage.py  blast_shown  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa  --shown true

#CDS fasta file: 
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_cds_from_genomic.fna  -m
python  manage.py  blast_utility  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_cds_from_genomic.fna  -p
python  manage.py  blast_shown  GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_cds_from_genomic.fna  --shown true

#For the genome assembly fasta file:
#stage
python manage.py addjbrowse GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna https://apollo2-stage-node1.nal.usda.gov/apollo/Culex_quinquefasciatus/jbrowse/
#prod   
python manage.py addjbrowse GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_genomic.fna https://apollo.nal.usda.gov/apollo/Culex_quinquefasciatus/jbrowse/

#Set up hmmer for peptide fasta fila: 
python manage.py addhmmer Culex quinquefasciatus -f /usr/local/i5k/media/blast/db/GCF_015732765.1_VPISU_Cqui_1.0_pri_paternal_translated_cds.faa -d 'Culex quinquefasciatus NCBI Annotation release 100, translated CDS'

[mpoelchau]

Finished.