~/gcc/groups/gonl

Directory structure of data management. On the Groningen cluster that would be target/gpfs2/gcc/groups/gonl Permission to read by gonl group, some folders also write.

• /tools
  • symlink to the /gcc/tools folder (except the folders you don't have access too)
• /resources
  • symlink to the /gcc/resources folder (except the folders you don't have access too)
• /home
  • one folder per member of this group
• /general
  • presentations, publications, other stuff
• /projects
  • /batchX
    • /rawdata
      • here is a list of fq.gz files
    • /results
      • /alignment
        • here is a list of bam files
      • /stats
        • here is one file per QC tool
      • /snp
        • here is one vcf file per analysis run
    • /logs
    • /intermediate_results
      • whatever is needed, will be empty at end of project
  • /gwas_data
    • /rawdata
      • original provided plink or genomestudio
    • /results
      • here the cleaned up genotypes in agreed upon format
    • /logs
  • /groningen_immunochip
    • /rawdata
    • /results
  • /pilot
    • /rawdata
      • /alignment
        • symlinks to the raw alignments used -> /first_batch/rawdata/some.aligned.cleaned.bam
    • /result
      • /snp
      • /indel
      • /cnv
    • logs
  • bgi
    • batchX: contains all the analysis data from BGI. Please see...for more information