http://icb.med.cornell.edu/wiki/index.php/Special:Recentchanges Track the most recent changes to the wiki on this page. en MediaWiki 1.6.8 Sat, 25 May 2013 21:45:19 GMT http://icb.med.cornell.edu/wiki/index.php/Elementolab/ChIPseeqer_Installation <p>/* Files you will need */ </p> <table border='0' width='98%' cellpadding='0' cellspacing='4' style="background-color: white;"> <tr> <td colspan='2' width='50%' align='center' style="background-color: white;">Revision as of 17:35, 23 May 2013</td> <td colspan='2' width='50%' align='center' style="background-color: white;">Current revision</td> </tr> <tr><td colspan="2" align="left"><strong>Line 71:</strong></td> <td colspan="2" align="left"><strong>Line 71:</strong></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;">|-</td><td> </td><td style="background: #eee; font-size: smaller;">|-</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;">| zebrafish (zv9)</td><td> </td><td style="background: #eee; font-size: smaller;">| zebrafish (zv9)</td></tr> <tr><td>-</td><td style="background: #ffa; font-size: smaller;">| http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/<span style="color: red; font-weight: bold;">mm9</span>.tar.gz</td><td>+</td><td style="background: #cfc; font-size: smaller;">| http://physiology.med.cornell.edu/faculty/elemento/lab/CS_files/<span style="color: red; font-weight: bold;">zv9</span>.tar.gz</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;">|-</td><td> </td><td style="background: #eee; font-size: smaller;">|-</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;">| saccharomyces cerevisiae</td><td> </td><td style="background: #eee; font-size: smaller;">| saccharomyces cerevisiae</td></tr> </table> Thu, 23 May 2013 17:35:07 GMT Eug2002 http://icb.med.cornell.edu/wiki/index.php/Talk:Elementolab/ChIPseeqer_Installation http://icb.med.cornell.edu/wiki/index.php/Elementolab/Cancer_Exome_Mutation_Discovery_pipeline <p>/* Loading mutations into the cBio portal */ </p> <table border='0' width='98%' cellpadding='0' cellspacing='4' style="background-color: white;"> <tr> <td colspan='2' width='50%' align='center' style="background-color: white;">Revision as of 15:53, 19 May 2013</td> <td colspan='2' width='50%' align='center' style="background-color: white;">Current revision</td> </tr> <tr><td colspan="2" align="left"><strong>Line 139:</strong></td> <td colspan="2" align="left"><strong>Line 139:</strong></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> <tr><td>-</td><td style="background: #ffa; font-size: smaller;">Login and load data</td><td>+</td><td style="background: #cfc; font-size: smaller;">Login and load data<span style="color: red; font-weight: bold;">:</span></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"> ssh -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com</td><td> </td><td style="background: #eee; font-size: smaller;"> ssh -i ~/.ssh/yourawskey.pem pmpca/ ec2-user@ec2-50-19-32-49.compute-1.amazonaws.com</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"> cd $PORTAL_HOME/core/src/main/scripts</td><td> </td><td style="background: #eee; font-size: smaller;"> cd $PORTAL_HOME/core/src/main/scripts</td></tr> <tr><td colspan="2" align="left"><strong>Line 149:</strong></td> <td colspan="2" align="left"><strong>Line 149:</strong></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"> sudo /etc/init.d/tomcat6 stop</td><td> </td><td style="background: #eee; font-size: smaller;"> sudo /etc/init.d/tomcat6 stop</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"> sudo /etc/init.d/tomcat6 start</td><td> </td><td style="background: #eee; font-size: smaller;"> sudo /etc/init.d/tomcat6 start</td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;"></td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;">To load CNAs: (data_CNA.txt being matrix of +1, 0, -1 etc for each gene, typically generated by GISTIC)</td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;"> $PORTAL_HOME/core/src/main/scripts/importProfileData.pl --data $PORTAL_DATA_HOME/studies/baca/data_CNA.txt \</td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;"> --meta $PORTAL_DATA_HOME/studies/baca/meta_CNA.txt --dbmsAction clobber</td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;"></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> </table> Sun, 19 May 2013 15:53:15 GMT Ole2001 http://icb.med.cornell.edu/wiki/index.php/Talk:Elementolab/Cancer_Exome_Mutation_Discovery_pipeline http://icb.med.cornell.edu/wiki/index.php/Elementolab/small_RNA-seq_pipeline <p></p> <table border='0' width='98%' cellpadding='0' cellspacing='4' style="background-color: white;"> <tr> <td colspan='2' width='50%' align='center' style="background-color: white;">Revision as of 17:57, 11 May 2013</td> <td colspan='2' width='50%' align='center' style="background-color: white;">Current revision</td> </tr> <tr><td colspan="2" align="left"><strong>Line 5:</strong></td> <td colspan="2" align="left"><strong>Line 5:</strong></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;">* remove adapters</td><td> </td><td style="background: #eee; font-size: smaller;">* remove adapters</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> <tr><td>-</td><td style="background: #ffa; font-size: smaller;">If the adapters have been masked:</td><td>+</td><td style="background: #cfc; font-size: smaller;">If the adapters have been masked<span style="color: red; font-weight: bold;">, eg by the core</span>:</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"> for f in s_*.txt.gz; do gr_5n &quot;perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/fastq_remove_N_adapters.pl $f&quot; --name=rem$f; done</td><td> </td><td style="background: #eee; font-size: smaller;"> for f in s_*.txt.gz; do gr_5n &quot;perl /home/ole2001/PROGRAMS/SNPseeqer/SCRIPTS/fastq_remove_N_adapters.pl $f&quot; --name=rem$f; done</td></tr> <tr><td colspan="2" align="left"><strong>Line 11:</strong></td> <td colspan="2" align="left"><strong>Line 11:</strong></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;">Otherwise use Smith-Waterman:</td><td> </td><td style="background: #eee; font-size: smaller;">Otherwise use Smith-Waterman:</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> <tr><td>-</td><td style="background: #ffa; font-size: smaller;"> for f in *.gz; do echo $f; gr_5n &quot;/home/ole2001/PROGRAMS/SMITH-WATER/remove_miRNA_adapter $f | gzip &gt; $f.noadapt.gz&quot; -name S$f ; done</td><td>+</td><td style="background: #cfc; font-size: smaller;"> for f in *.gz; do echo $f; gr_5n &quot;/home/ole2001/PROGRAMS/SMITH-WATER/remove_miRNA_adapter <span style="color: red; font-weight: bold;">-fastqfile </span>$f | gzip &gt; $f.noadapt.gz&quot; -name S$f ; done</td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> <tr><td> </td><td style="background: #eee; font-size: smaller;"></td><td> </td><td style="background: #eee; font-size: smaller;"></td></tr> </table> Sat, 11 May 2013 17:57:27 GMT Ole2001 http://icb.med.cornell.edu/wiki/index.php/Talk:Elementolab/small_RNA-seq_pipeline