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filemanagement.md

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Machines

  • biowulf2.nih.gov
  • biowulf.nih.gov
  • helix.nih.gov
  • TGEN server = 10.133.130.41
  • aphasia.nci.nih.gov

##File locations

Raw data

Fastq files

Demultiplexed FASTQ files are in stored on the TGEN server. Paths conform to a pattern like this:

/projects/pipeline/Clinomics/RUN_DIRECTORY_NAME/Project_Clinomics_Exome/SAMPLENAME/*fastq.gz

Run folders

The run folders contain the raw data (bcl files). They are stored on the TGEN server in the following two paths:

  • /projects/HiSeq_result
  • /projects/NextSeq_result

Metadata

  • Excel file containing sample information
    • TGEN
      • NEED THIS LOCATION

Processed data

  • Processed data (BAM, VCF, etc)
    • TGEN
      • /projects/clinomics/
      • I created this for running the pipeline and hence the bam/vcf/etc locations should be same as /data/Clinomics/Analysis/ on biowulf.