http://bmcwiki.mit.edu/index.php?action=history&feed=atom&title=BioMicroCenter%3ADataArchiving 2026-04-29T03:18:48Z Revision history for this page on the wiki MediaWiki 1.43.1 http://bmcwiki.mit.edu/index.php?title=BioMicroCenter:DataArchiving&diff=46&oldid=prev 2009-11-18T12:56:40Z

<p>New page: {{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 SplitBar...</p> <p><b>New page</b></p><div>{{BioMicroCenter}}<br /> <br /> PROTOCOL TO DISTRIBUTE AND ARCHIVE ILLUMINA RUNS FROM BIOMICRO CENTER<br /> <br /> 1. IF NEEDED, SPLIT BARCODES:<br /> cd /mnt/biomicro/biomicro/SL_Code/Solexa_Scripts/<br /> perl SplitBarcodes.pl &lt;PathToGerald&gt; s_&lt;N&gt; &lt;&lt;LIST OF BARCODES&gt;&gt;<br /> <br /> wait for the code to finish.<br /> <br /> 2. RUN TagCount.pl<br /> cd /mnt/biomicro/biomicro/SL_Code/Solexa_Scripts/<br /> perl TagCount.pl &lt;PathToGerald&gt; &lt;PathToGerald&gt;/TagCount.xls &amp;<br /> <br /> wait for the code to finish.<br /> <br /> 3. CREATE A RENAMING FILE<br /> x x x /mnt/biomicro/biomicro/PHIX_runs/DATE/<br /> x x x /mnt/bmc-pub1/public/Illumina/LAB/DATE/<br /> s_N DATE_ID_USER_LAB_LN GENOME /mnt/bmc-pub1/public/Illumina/LAB/DATE/<br /> <br /> * N = 1-8. If you split barcodes, every barcode should be included.<br /> * DATE = date run initiated (can be found in the filemaker database)<br /> * labs with accounts in pub1/pub3 can be written to directly.<br /> <br /> example (/mnt/biomicro/biomicro/090828.txt):<br /> x x x /mnt/biomicro/biomicro/PHIX_runs/090831/<br /> x x x /mnt/boyerpub2/Illumina/090831/<br /> s_1 090831_V6.5_sharif_Boyer_L1 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_1AAGGT 090831_V6.5aaggt_sharif_Boyer_L1 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_1CATGT 090831_V6.5catgt_sharif_Boyer_L1 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_1GCTGT 090831_V6.5gctgt_sharif_Boyer_L1 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_1TGAGT 090831_V6.5tgagt_sharif_Boyer_L1 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_1NM 090831_V6.5nm_sharif_Boyer_L1 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_2 090831_miPS_sharif_Boyer_L2 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_2AAGGT 090831_miPSaaggt_sharif_Boyer_L2 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_2CATGT 090831_miPScatgt_sharif_Boyer_L2 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_2GCTGT 090831_miPSgctgt_sharif_Boyer_L2 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_2TGAGT 090831_miPStgagt_sharif_Boyer_L2 mm9 /mnt/boyerpub2/Illumina/090831/<br /> s_2NM 090831_miPSnm_sharif_Boyer_L2 mm9 /mnt/boyerpub2/Illumina/090831/<br /> <br /> <br /> 4. RUN RENAMING/DISTRIBUTION CODE<br /> <br /> cd /mnt/biomicro/biomicro/SL_Code/Solexa_Scripts/<br /> perl BMC_Solexa_Storage_v14.pl &lt;PathToGerald&gt; &lt;PathToTextFile&gt; 0 s|p &amp;<br /> <br /> * use &#039;&#039;&#039;s&#039;&#039;&#039; for single end and &#039;&#039;&#039;p&#039;&#039;&#039; for paired end samples<br /> <br /> 5. DATA ARCHIVING<br /> <br /> cd /mnt/bmc-pub2/current/grunN/0****/DATA/<br /> tar -czf /mnt/bmc-9/?/DATE_FLOWCELLID_FILEMAKERRECORD.tgz Intensities/ &amp;<br /> <br /> 6. AFTER CONFIRMING DOWNLOAD<br /> <br /> cd /mnt/bmc-pub2/current/grunN/<br /> rm -fR * &amp;<br /> cd /mnt/bmc-pub1/public/Illumina/LAB/DATE<br /> tar -czf DATE.tgz DATE/ &amp;</div>

imported>Stuart S. Levine