====== TSD p33 directory structure ======

==== /tsd/p33/home ====
This is your personal area. Every project-member have their own private folder here.  

==== /tsd/p33/data ====

This is our main storage. Directory containing files the computing cluster needs **no** access to.\\
See how to map directory first time[[https://www.uio.no/english/services/it/research/sensitive-data/use-tsd/directories-files/|here]].

  * **''/tsd/p33/data/''**
    * ''colossus/'' deprecated cluster-accessible container
    * **''durable/''** backed-up container
      * ''characters/'' personal p33-users directories
      * ''drift/'' booking and log of participants
      * ''external/'' data from sources other than NORMENT
      * ''file-api/'' contains files that were uploaded to TSD
      * ''file-import/'' contains files that were uploaded to TSD by using the web form
      * ''groups/'' directories dedicated to specific work groups; if you've got data that you feel does not belong into any of these groups please talk to an administrator.
        * ''biostat/''[[tsd_directory_structure#biostat_details|details]]
        * ''clinical/'' [[tsd_directory_structure#clinical_details|details]]
        * ''cognition/''
        * ''imaging/''
        * ''stemcell/''
    * ''no-backup/'' less important files that do not require backup


==== /cluster/projects/p33 ====

Files stored here can be accessed from the login nodes and the computing cluster.

  * **''/cluster/projects/p33''**
      * ''groups/'' same as ''/tsd/p33/data/durable/groups''
        * ''biostat/'' [[tsd_directory_structure#biostat_details|details]]
        * ''clinical/'' [[tsd_directory_structure#clinical_details|details]]
        * ''cognition/''
        * ''imaging/''
        * ''stemcell/''
      * ''nordat/'' internal files of general interest (e.g. polygenic scores)
      * ''shared/'' external files of general interest (e.g. UK-biobank stuff)
      * ''tmp/'' temporary storage
      * ''users/'' personal p33-users directories


=== Details ===


Below are more details on the individual group directories


=== biostat details ===

  * ''genetics/''
    * ''external/'' -- data from external sources like 1KG or HRC
    * ''gwas/'' -- genome-wide association studies summary statistics
    * ''idat/'' -- intensity files from chip-genotyping
    * ''imputed/'' -- imputed genotypes
      * ''cur'' -> latest freeze 
      * ''YYYYMMDD/'' -- freeze from YYYY.MM.DD
        * ''stage1''/ -- chip-genotyping batch-wise imputation
          * ''<Batchname>/''
            * ''bcf/'' -- binary variant call format genotypes
              * ''qc0/'' -- next-to-unprocessed imputed genotypes (R2>0.01)
                * ''chr1.bcf'' ... ''chr25.bcf''
              * ''qc1/'' -- high quality imputed genotypes
                * ''chr1.bcf'' ... ''chr25.bcf''
            * ''bed/'' -- plink binary file triplet format high quality imputed genotypes
              * ''chr1.bed'' ... ''chr25.bed''
              * ''chr1.bim'' ... ''chr25.bim''
              * ''chr1.fam'' ... ''chr25.fam''
            * ''bio.txt'' -- individuals genotype QC history
            * ''.i/'' -- pre-imputation QC and imputation intermediate files
              * ''im/'' -- phasing and imputation intermediate files
              * ''qc/'' -- qc intermediate files
        * ''stage2''/ -- (not implemented, yet)
          * ''bcf/''
              * ''qc0/''
                * ''chr1.bcf'' ... ''chr25.bcf''
              * ''qc1/''
                * ''chr1.bcf'' ... ''chr25.bcf''
          * ''bed/''
            * ''chr1.bed'' ... ''chr25.bed''
            * ''chr1.bim'' ... ''chr25.bim''
            * ''chr1.fam'' ... ''chr25.fam''
          * ''bio.txt''
        * ''stage3''/ -- (not implemented, yet)
          * ''bcf/''
              * ''qc0/''
                * ''chr1.bcf'' ... ''chr25.bcf''
              * ''qc1/''
                * ''chr1.bcf'' ... ''chr25.bcf''
          * ''bed/''
            * ''chr1.bed'' ... ''chr25.bed''
            * ''chr1.bim'' ... ''chr25.bim''
            * ''chr1.fam'' ... ''chr25.fam''
          * ''bio.txt''
          * ''.i/''
            * ''im/''
            * ''qc/''
      * ...
    * ''pgs/'' -- polygenic scores
      * ''cur'' -> latest freeze
      * ''YYYYMMDD/'' -- freeze from YYYY.MM.DD
        * ''<SOURCE>_<PHENO>_<YEAR>[_<...>]''
          * ''pgs_<p-value_threshold>.csv''
          * ...
        * ...
        * ''variants_included.txt'' -- log excerpts with the number of variants included per batch
      * ...
    * ''rawdata/'' -- ex-silico derived data
    * ''projects/''
    * ''software/''

==== clinical details ====

  * ''blood/'' -- data from biobank FHI
    * ''immune/'' -- data from Rikshospitalet
  * ''genetics/'' -- PGS output for merging wPhenotypes
    * ''Genotype_to_database/'' -- GWAS overview
    * ''LRP_Genetics_Database/'' -- data from external sources like Demgene(Lavinia)
  * ''projects/''
    * ''bergen_bp/'' -- data from Bergen Bipolar cohort
    * ''blood_donors/'' -- data from HC donor cohort
    * ''brain/'' -- data from the BRAIN Bipolar project
    * ''bupgen/'' -- data from the BupGen Autism/rare disease project      
    * ''clozapine/'' -- data from the CLOZ cohort 
    * ''demgene/'' -- data from the DemGene project
    * ''ephaps/'' -- data from the EPHAPS Vestfold project
    * ''lifespan/'' -- data from the LifeSpan cohort
    * ''medgen/'' -- data from the MedGen cohort
    * ''noda/'' -- files used in the NoDa database
    * ''nonstop/'' -- data from the NONSTOP project
    * ''norcor/'' -- data from the NorCor cohort
    * ''nordoc/'' -- data from the NorDoc cohort
    * ''stroke_mri/'' -- data from the Ulleval STROKE cohort
    * ''tips/'' -- data from the TIPS project
    * ''top/'' -- data from the TOP/NORMENT project
      * ''biobank/'' -- Blood samples and biobank overview
      * ''cleanfiles/'' -- phenotype data from the clinical database☚
      * ''mindag/'' -- data from the MinDag app
      * ''nettskjema/'' -- data from web-forms through Nettskjema
      * ''longitudinal'' -- data for the clinical follow-up group

