Changes between Version 8 and Version 9 of BGIDatasets


Ignore:
Timestamp:
Jun 30, 2011 10:06:08 AM (14 years ago)
Author:
Barbera van Schaik
Comment:

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  • BGIDatasets

    v8 v9  
    1 = '''BGI datasets''' =
     1= '''Overview BGI datasets''' =
     2
    23TODO: More info on statistic and how to access the dataset will be added here.
    3 
    4  * Pilot phase:  60 samples, 180 lanes. 183 lanes in total due to rerun.
    5  * 2st batch: 90 samples, 295 lanes.
    6  * 3rd batch: 222 samples, 683 lanes, 10TB
    7 
    84BGI will shared with us: SNP calling results (VCF), SOAP format for indels.
    9 
    10 = '''Data location''' =
    115
    126|| '''Batch''' || '''Samples''' || '''Lanes''' || '''Size''' || '''Groningen storage''' || '''Grid storage (VO)''' || '''Storage additional sites''' || '''Analysis site''' || '''Status''' ||
    … …  
    1711|| 5th batch || 153 || || || no || no || || || not on storage yet ||
    1812|| 6th batch || 10 || || || no || || || || not arrived yet ||
     13
     14== '''Directories''' ==
     15
     16'''1st batch'''
     17* Groningen
     18   * Raw data (fastq)
     19   * Results
     20* Grid (vlemed)
     21   * Raw data SRM (fastq) srm://srm.grid.sara.nl:8443/pnfs/grid.sara.nl/data/vlemed/gvnl/data (access to members of vlemed/gvnl)
     22   * Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data (access closed)
     23   * Results LFC lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data/bam/markduplicates/realignment/fixmates/recalibrate/sorted (access closed)
     24
     25'''2nd batch'''
     26* Groningen
     27   * Raw data (fastq)
     28   * Results (bam)
     29* Grid (vlemed)
     30   * 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)
     31   * Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data (access closed)
     32   * Results LFC lfn://lfc.grid.sara.nl:5010/grid/vlemed/gvnl/data/bam/markduplicates/realignment/fixmates/recalibrate/sorted (access closed)
     33
     34
     35'''3rd batch'''
     36* Groningen
     37   * Raw data (fastq)
     38   * Results
     39
     40
     41'''4th batch'''
     42* Groningen
     43   * Raw data (fastq)
     44   * Results
     45* Grid (bbmri.nl)
     46   * 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)
     47   * Raw data LFC (fastq) lfn://lfc.grid.sara.nl:5010/grid/bbmri.nl/gonl/data/input (access to members of bbmri.nl VO)
     48   * Results LFC lfn://lfc.grid.sara.nl:5010/grid/bbmri.nl/gonl/data/output (access to members of bbmri.nl VO)