wiki:BGIDatasets

Version 9 (modified by Barbera van Schaik, 13 years ago) (diff)

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Overview BGI datasets

TODO: More info on statistic and how to access the dataset will be added here. BGI will shared with us: SNP calling results (VCF), SOAP format for indels.

Batch Samples Lanes Size Groningen storage Grid storage (VO) Storage additional sites Analysis site Status
1st batch aka Pilot phase 60 183 yes yes (vlemed) UMGC, AMC (for comparison) aligned, in progress
2st batch 90 295 yes yes (vlemed) AMC in progress
3rd batch 222 683 10TB yes no UMGC in progress
4th batch 235 630 10TB yes yes (bbmri.nl) Hubrecht, EMC LUMC/TUdelft, UMGC, Hubrecht, EMC in progress
5th batch 153 no no not on storage yet
6th batch 10 no not arrived yet

Directories

1st batch

  • Groningen
    • Raw data (fastq)
    • Results
  • Grid (vlemed)
    • Raw data SRM (fastq) srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/vlemed/gvnl/data (access to members of vlemed/gvnl)
    • Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data (access closed)
    • Results LFC lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data/bam/markduplicates/realignment/fixmates/recalibrate/sorted (access closed)

2nd batch

  • Groningen
    • Raw data (fastq)
    • Results (bam)
  • Grid (vlemed)
    • Raw data SRM (fastq) srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/vlemed/gvnl/data (access to members of vlemed/gvnl VO)
    • Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data (access closed)
    • Results LFC lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data/bam/markduplicates/realignment/fixmates/recalibrate/sorted (access closed)

3rd batch

  • Groningen
    • Raw data (fastq)
    • Results

4th batch

  • Groningen
    • Raw data (fastq)
    • Results
  • Grid (bbmri.nl)
    • Raw data SRM (fastq) srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/bbmri.nl/fourth_batch (access to members of bbmri.nl VO)
    • Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/bbmri.nl/gonl/data/input (access to members of bbmri.nl VO)
    • Results LFC lfn://lfc.grid.sara.nl:5010/grid/bbmri.nl/gonl/data/output (access to members of bbmri.nl VO)