SLab:File System Layout

Schuster Lab Root Directory

• /afs/bx.psu.edu/depot/data/schuster_lab

The Schuster Lab's data can be found in the /afs/bx.psu.edu/depot/data/schuster_lab directory.

Sequencing Directory

• /afs/bx.psu.edu/depot/data/schuster_lab/sequencing

Access to all of the Schuster Lab's sequencing data is through the sequencing directory. This directory contains archived run directories as well as directories for runs that are currently in progress.

archive

• /afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/
  • 454/
    • by_date/
    • flat/
    • by_project/
  • illumina/
    • by_date/
    • flat/
    • by_project/

The sequencing archive directory contains a read-only archive of all sequencing runs and contains a sub directory for each sequencing platform. Within each sequencing platform directory, runs are organized by the date the run was started.

Directory for the 454 R_2010_01_22_16_12_03_FLX11080447_John_ChineseChestnut_Run9 run.

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/454/by_date/2010/2010_01_22/R_2010_01_22_16_12_03_FLX11080447_John_ChineseChestnut_Run9

Directory for the Illumina 100201_HWUSI-EAS610_0006 run.

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/illumina/by_date/2010/2010_02_01/100201_HWUSI-EAS610_0006

In addition, each sequencing platform directory contains a flat/ sub directory that contains symbolic links to every run for that platform.

flat/ directory for the 454 R_2010_01_22_16_12_03_FLX11080447_John_ChineseChestnut_Run9 run.

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/454/flat/R_2010_01_22_16_12_03_FLX11080447_John_ChineseChestnut_Run9

flat/ directory for the Illumina 100201_HWUSI-EAS610_0006 run.

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/illumina/flat/100201_HWUSI-EAS610_0006

The by_project/ directories can be used to organize all runs for a specific project

For the chestnut project:

/afs/bx.psu.edu/depot/data/schuster_lab/sequencing/archive/illumina/by_project/chestnut/runs/100211_HWUSI-EAS610_0005

staging and temp

• /afs/bx.psu.edu/depot/data/schuster_lab/sequencing/staging/
  • 454/
  • illumina/
• /afs/bx.psu.edu/depot/data/schuster_lab/sequencing/temp/
  • 454/
  • illumina

The sequencing staging and sequencing temp directories are used to hold sequencing runs that are still being processed (either the run is not finished, or signal processing is being done).

support

• /afs/bx.psu.edu/depot/data/schuster_lab/sequencing/support/
  • 454/
  • illumina/

The sequencing support directory contains manuals, software, and reference genomes used during sequencing and sequence processing.

Projects Directory

• /afs/bx.psu.edu/depot/data/schuster_lab/projects

Users Directory

• /afs/bx.psu.edu/depot/data/schuster_lab/users