wiki:BIOS_FileBackups

Version 1 (modified by jamverlouw, 8 years ago) (diff)

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This page describes which BIOS files are backed up and where on the SRM of life science grid.

The following directories are copied to the SRM backup folder where all files are backed up by SURFsara on their tapes. 

 /pnfs/grid.sara.nl/data/bbmri.nl/RP3/RNASeq
 /pnfs/grid.sara.nl/data/bbmri.nl/RP3/IlluminaHumanMethylation450k
 /pnfs/grid.sara.nl/data/bbmri.nl/RP3/Phenotypes
 /pnfs/grid.sara.nl/data/bbmri.nl/RP3/GWAS_ImputationGoNLv4/
 /pnfs/grid.sara.nl/data/bbmri.nl/RP3/GWAS_ImputationGoNLv5/

RNAseq

Raw data from ErasmusMC

  • Files: <flowcell ID>-<lane ID>-<index ID>_R1.fq.gz, <flowcell ID>-<lane ID>-<index ID>_R2.fq.gz, <flowcell ID>-<lane ID>-<index ID>-remaining.tar.gz
  • Location
    • srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/backup/RP3/RNASeq
  • Backup log
    • 2014-01-21: 4888 files are backed up. only fastq files. 2444 samples? Adler checksum is verified but not md5.

Results of standard analysis using LSG pipeline

  • Files: *.exon.count, *.transcript.count, *.gene.count, *.sorted.bam, *.run.log.
  • Location
  • Backup log

Methylation

Raw data from ErasmusMC

  • Files: <biobank>_sample_sheet.csv, *.idat
  • Location
    • srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/backup/RP3/IlluminaHumanMethylation450k/LL_sample_sheet.csv
    • srm://srm.grid.sara.nl/pnfs/grid.sara.nl/data/bbmri.nl/backup/RP3/IlluminaHumanMethylation450k/9285451044/9285451044_R03C02_Grn.i
  • Backup log

Phenotype