Editing BioMicroCenter:DataArchiving

{{BioMicroCenter}}

PROTOCOL TO DISTRIBUTE AND ARCHIVE ILLUMINA RUNS FROM BIOMICRO CENTER

1. IF NEEDED, SPLIT BARCODES:
  cd /mnt/biomicro/biomicro/SL_Code/Solexa_Scripts/
  perl SplitBarcodes.pl <PathToGerald> s_<N> <<LIST OF BARCODES>>

wait for the code to finish.

2. RUN TagCount.pl
  cd /mnt/biomicro/biomicro/SL_Code/Solexa_Scripts/
  perl TagCount.pl <PathToGerald> <PathToGerald>/TagCount.xls &

wait for the code to finish.

3. CREATE A RENAMING FILE
  x       x       x       /mnt/biomicro/biomicro/PHIX_runs/DATE/
  x       x       x       /mnt/bmc-pub1/public/Illumina/LAB/DATE/
  s_N     DATE_ID_USER_LAB_LN        GENOME    /mnt/bmc-pub1/public/Illumina/LAB/DATE/

* N = 1-8. If you split barcodes, every barcode should be included.
* DATE = date run initiated (can be found in the filemaker database)
* labs with accounts in pub1/pub3 can be written to directly.

example (/mnt/biomicro/biomicro/090828.txt):
  x       x       x       /mnt/biomicro/biomicro/PHIX_runs/090831/
  x       x       x       /mnt/boyerpub2/Illumina/090831/
  s_1     090831_V6.5_sharif_Boyer_L1     mm9     /mnt/boyerpub2/Illumina/090831/
  s_1AAGGT        090831_V6.5aaggt_sharif_Boyer_L1        mm9     /mnt/boyerpub2/Illumina/090831/
  s_1CATGT        090831_V6.5catgt_sharif_Boyer_L1        mm9     /mnt/boyerpub2/Illumina/090831/
  s_1GCTGT        090831_V6.5gctgt_sharif_Boyer_L1        mm9     /mnt/boyerpub2/Illumina/090831/
  s_1TGAGT        090831_V6.5tgagt_sharif_Boyer_L1        mm9     /mnt/boyerpub2/Illumina/090831/
  s_1NM   090831_V6.5nm_sharif_Boyer_L1   mm9     /mnt/boyerpub2/Illumina/090831/
  s_2     090831_miPS_sharif_Boyer_L2     mm9     /mnt/boyerpub2/Illumina/090831/
  s_2AAGGT        090831_miPSaaggt_sharif_Boyer_L2        mm9     /mnt/boyerpub2/Illumina/090831/
  s_2CATGT        090831_miPScatgt_sharif_Boyer_L2        mm9     /mnt/boyerpub2/Illumina/090831/
  s_2GCTGT        090831_miPSgctgt_sharif_Boyer_L2        mm9     /mnt/boyerpub2/Illumina/090831/
  s_2TGAGT        090831_miPStgagt_sharif_Boyer_L2        mm9     /mnt/boyerpub2/Illumina/090831/
  s_2NM   090831_miPSnm_sharif_Boyer_L2   mm9     /mnt/boyerpub2/Illumina/090831/


4. RUN RENAMING/DISTRIBUTION CODE

  cd /mnt/biomicro/biomicro/SL_Code/Solexa_Scripts/
  perl BMC_Solexa_Storage_v14.pl <PathToGerald> <PathToTextFile> 0 s|p &

* use '''s''' for single end and '''p''' for paired end samples

5. DATA ARCHIVING

   cd /mnt/bmc-pub2/current/grunN/0****/DATA/
   tar -czf /mnt/bmc-9/?/DATE_FLOWCELLID_FILEMAKERRECORD.tgz Intensities/ &

6. AFTER CONFIRMING DOWNLOAD

   cd /mnt/bmc-pub2/current/grunN/
   rm -fR * &
   cd /mnt/bmc-pub1/public/Illumina/LAB/DATE
   tar -czf DATE.tgz DATE/ &