HIRIS_project

HIV-1 Reservoirs Integration Sites

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Instalation

Clone GitHub repository
Copy .env.TEMPLATE to .env
Generate a secret key and put into .env
update docker-compose.yml lines 11 and 31 to change the PostgreSQL password from mypassword to something more secure. The password must match in both places

Initial loading of genome data

Add ref_GRCh38.p2_top_level.gff3 Add Homo_sapiens.gene_info_modified.tsv Add chr_accessions_GRCh38_modified.tsv

Set ref_GRCh38.p2_top_level.gff3 as primary

Link ref_GRCh38.p2_top_level.gff3 -> Dbxref with

• Homo_sapiens.gene_info_modified.tsv -> GeneID

Link ref_GRCh38.p2_top_level.gff3 -> seqid with

• chr_accessions_GRCh38_modified.tsv -> RefSeq Accession.version

Specify:

• Genome Species = Homo Sapiens
• Genome Version = GRCh38.p2

Set up import fields:

• Gene Type

  • Gene Type Name = Homo_sapiens.gene_info_modified.tsv -> type_of_gene

• Feature Type

  • Feature Type Name = ref_GRCh38.p2_top_level.gff3 -> featuretype

• Feature

  • Feature Name = ref_GRCh38.p2_top_level.gff3 -> Name
  • External Gene ID = Split Field, Homo_sapiens.gene_info_modified.tsv -> GeneID, Using Character -> :, keeping value in position -> 2

• Feature Location

  • Chromosome = chr_accessions_GRCh38_modified.tsv -> Chromosome
  • Landmark = ref_GRCh38.p2_top_level.gff3 -> seqid
  • Feature Start = ref_GRCh38.p2_top_level.gff3 -> start
  • Feature End = ref_GRCh38.p2_top_level.gff3 -> end
  • Feature Orientation = ref_GRCh38.p2_top_level.gff3 -> strand

Intial loading of previous ISDB data

Add ISDB_Data.csv

Set up import fields:

• Genome Version

  • Genome Version Name: Select "GRCh38.p2" under "Values from Genome Version Name"

• Data Set

  • Data Set Name: data_set_name

• Publication

  • Publication Pubmed ID: publication_pubmed_id

• Data Set Source

  • Document Pubmed ID: document_pubmed_id
  • Document Uri: document_uri

• Subject

  • Subject Identifier: subject_identifier

• Subject Data

  • Click "Unused"

• Sample *Sample Name: Set to "No Data"

• Sample Data

  • date
    • Select "culture" from drop down
    • Click "Add"
    • Select "culture" from dropdown in Key column
  • Repeat for
    • culture_day
    • date
    • disease
    • genbank
    • original_id
    • provirus_activity
    • pubmed_id
    • replicates
    • tissue
    • tissue_url
    • type
    • visit
    • years_on_art

• Preparation

  • Preparation Description: preparation_description

• Sequencing Method

  • Sequencing Method Name: Set to "No Data"
  • Sequencing Method Description: Set to "No Data"

• Integration Environment

  • Integration Environment Name: integration_environment_name

• Integration

  • Integration Name: Set to "No Data"
  • Ltr: ltr
  • Multiple Integration: Set to "No Data"
  • Multiple Integration Count: Set to "No Data"
  • Sequence: sequence
  • Junction 5P: junction_5p
  • Junction 3P: Set to "No Data"
  • Sequence Name: sequence_name
  • Sequence Uri: sequence_uri
  • Ltr Sequence: Set to "No Data"
  • Breakpoint Sequence: Set to "No Data"
  • Umi Sequence: Set to "No Data"
  • Ltr Sequence 5P: Set to "No Data"
  • Breakpoint Sequence 5P: Set to "No Data"
  • Umi Sequence 5P: Set to "No Data"
  • Ltr Sequence 3p: Set to "No Data"
  • Breakpoint Sequence 3p: Set to "No Data"
  • Umi Sequence 3P: Set to "No Data"
  • Provirus Sequence: Set to "No Data"
  • Replicate: Set to "No Data"
  • Replicates: Set to "No Data"
  • Note: note

• Integration Location

  • Landmark: "Translate Chromosome To Ascession ID" Chromosome: landmark
  • Location: location
  • Breakpoint Landmark: Set to "No Data"
  • Breakpoint Location: Set to "No Data"
  • Landmark 5P: Set to "No Data"
  • Location 5P: Set to "No Data"
  • Breakpoint Landmark 5P: Set to "No Data"
  • Breakpoint Location 5P: Set to "No Data"
  • Landmark 3P: Set to "No Data"
  • Location 3p: Set to "No Data"
  • Breakpoint Landmark 3P: Set to "No Data"
  • Breakpoint Location 3P: Set to "No Data"
  • Orientation In Landmark: orientation_in_landmark

• Blast Info

  • Identity: identity
  • Q Start: q_start
  • Gaps: gaps
  • Score: Set to "No Data"

Run management command "process_after_import" root@b7b166e095bd:/hiris# ./manage.py process_after_import