~/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
  • All software, scripts and tools used to process the data
• /resources
  • All resources needed for data processing, including genome references, dbSNP releases, etc.
• /home
  • one private 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
      • A set of compressed files containing the plain text data and md5 files for downloading purpose. These are named as follows: timestamp.BGI.batchX.data_type.hg1X.data_format.tar.bz2. All plain text data should be available as a compressed file, including but not limited to: CNV, InDel, InDel annotations, SNP, SNP annotation. Some of these are available in multiple formats; see BGI data page for more explanation about the BGI data and its formats.md5 checksum files is also available for all files.
    • batchX/bam OR batchX/alignment
      • The BAM files aligned by BGI
    • batchX/CNV
      • CNVs in CNV Detector format. If you want to download for all samples, please download the compressed archive from batchX/
    • batchX/indel
      • InDels in samtools pileup format. If you want to download for all samples, please download the compressed archive from batchX/
    • batchX/indel_annotation
      • Indels annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    • batchX/SNP
      • SNP in SOAPsnp format. If you want to download for all samples, please download the compressed archive from batchX/
    • batchX/SNP_annotation
      • SNP annotations in GFF format. If you want to download for all samples, please download the compressed archive from batchX/
    • batchX/vcf_format/CNV
      • CNV in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    • batchX/vcf_format/indel
      • Indel in VCF format. If you want to download for all samples, please download the compressed archive from batchX/
    • batchX/vcf_format/SNP
      • SNP in VCF format. If you want to download for all samples, please download the compressed archive from batchX/