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 Fri, 29 Mar 2013 10:22:58 GMT http://icb.med.cornell.edu/wiki/index.php/Elementolab/Cancer_Exome_Mutation_Discovery_pipeline <p>/* Alignment */ </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 17:53, 28 March 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 23:</strong></td> <td colspan="2" align="left"><strong>Line 23:</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;">(use --submit=0 to see the PBS script without submitting)</td><td> </td><td style="background: #eee; font-size: smaller;">(use --submit=0 to see the PBS script without submitting)</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;"></td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;">If you have multiple samples compared to the same reference, you can produce a table to summarize the results using the following command:</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;"> perl ~/PROGRAMS/SNPseeqer/SCRIPTS/TargetID_summarizeClones.pl --clonefile=desc_samples.txt --qspv=0.1 --nohmz=0 --zeropar=1 --fdr=0.05 --mincnt=1</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;">where desc_samples.txt is a tab-delimited file containing sample ID and .cmp file, for example </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;"> 1 ./s_1_sequence.txt.hg18.sorted.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs.cmp</td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;"> 2 ./s_2_sequence.txt.hg18.sorted.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs.cmp</td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;"> 3 ./s_3_sequence.txt.hg18.sorted.sam.SNVs.dbSNP.annot.1KG.kmut.TFBS.Cons.flseq.qs.cmp</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;">=SNV analysis=</td><td> </td><td style="background: #eee; font-size: smaller;">=SNV analysis=</td></tr> </table> Thu, 28 Mar 2013 17:53:31 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/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 14:42, 22 March 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 49:</strong></td> <td colspan="2" align="left"><strong>Line 49:</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;"> perl ~/PROGRAMS/SNPseeqer/SCRIPTS/RNAseq_summarize.pl --dirs=. --outfile=mat_vivek_RNAseq.txt --species=mouse --genes=1</td><td> </td><td style="background: #eee; font-size: smaller;"> perl ~/PROGRAMS/SNPseeqer/SCRIPTS/RNAseq_summarize.pl --dirs=. --outfile=mat_vivek_RNAseq.txt --species=mouse --genes=1</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 change sample names, use </td></tr> <tr><td colspan="2">&nbsp;</td><td>+</td><td style="background: #cfc; font-size: smaller;"> --sampleinfo=tablenames.txt # tab delim, first col is core name, second col is full name</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;">* '''to make BigWig tracks, upload to lab's web server; will write track data to screen by default'''</td><td> </td><td style="background: #eee; font-size: smaller;">* '''to make BigWig tracks, upload to lab's web server; will write track data to screen by default'''</td></tr> </table> Fri, 22 Mar 2013 14:42:06 GMT Ole2001 http://icb.med.cornell.edu/wiki/index.php/Talk:Elementolab/RNA-seq_pipeline