HPV project setup

  • Use seqbank to query paths for data 
select server_experiment.id, extra_details, results_path, server_celltype.type from server_project 
join server_experiment on server_project.id=server_experiment.project_id 
join server_experimentanalysis on server_experiment.id=server_experimentanalysis.experiment_id
join server_celltype on server_experiment.cell_type_id=server_celltype.id
where server_project.name="vTR_HPV"
  • No Transient (according to Phil [because of EBV paper])
  • Only use stable
  • vTR_​control (HCT116-CL0168) FLpIn293

/integrative_​analysis/ChIP/ATAC

TODO Nextflow [0/3]

  • ☐ Setup project directory
    • What's the deal with the existing HPV directory?
  • ☐ Nix container setup
  • ☐ GitHub

TODO Early analysis

  • Collect MultiQC outputs (should be in results directory from seqbank)
  • wurl can be used to view multiqc reports
  • Data quality "Pass" (exact)
  • mixtape deseq pipeline (20% is used in the EBV paper)
  • differential between all four strains (HPV strains) and high risk and low risk
  • Look for BAM files in ATAC
  • narrowPeak files (idr_​conservative (convervation across replicates))

Ask about transient tests

  • Only HPV 16

Make spreadsheet with urls to every multiQC report

  • Use SQL query, then post process with wurl