| mutsig2cluster_new1 sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigWithNozzleReport/COADREAD/1604664/3.MutSigRun.Finished/COADREAD.sample_sig_gene_table.txt |
| Correlate_Clinical_Clusters_onlysig2 clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD/1551751/1.GDAC_clinicalDataPicker.Finished/COADREAD.clin.merged.picked.txt |
| Correlate_Clinical_Clusters_onlysig2 filter cluster smaller than | 3 |
| Correlate_Clinical_Clusters_onlysig2 figure height | 5 |
| Correlate_Clinical_Clusters_onlysig2 figure width | 9 |
| Correlate_Clinical_Clusters_onlysig2 survival legend position | OUT |
| Correlate_Clinical_Clusters_onlysig2 pvalue cutoff | 1 |
| Correlate_Clinical_Clusters_onlysig2 qvalue cutoff | 0.25 |
| Correlate_Clinical_Clusters_onlysig2 make figure | ONLYSIG |
| Correlate_Clinical_Clusters_onlysig2 nozzle ver | Nozzle.R1 |
| Execution Times: | |
| Submitted: | 23:01:56 05-08-12 |
| Completed: | |
| Elapsed: | 00 hrs 01 mins 56 secs |
step 1. mutsig2cluster_new [id: 143184] Convert mutsig results to cluster files
urn:lsid:broadinstitute.org:cancer.genome.analysis:00336:4
| sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigWithNozzleReport/COADREAD/1604664/3.MutSigRun.Finished/COADREAD.sample_sig_gene_table.txt |
| maf file | |
| sig gene file | |
| sig gene q cutoff | 0.01 |
| output name |
| Output Files: | |
| COADREAD.mutsig.cluster.txt | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 23:01:56 05-08-12 |
| Completed: | 23:02:15 05-08-12 |
| Elapsed: | 00 hrs 00 mins 18 secs |
step 2. Correlate_Clinical_Clusters_onlysig [id: 143185]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:32
| cluster label file | COADREAD.mutsig.cluster.txt |
| clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPickerPipeline/COADREAD/1551751/1.GDAC_clinicalDataPicker.Finished/COADREAD.clin.merged.picked.txt |
| features used | ALL |
| filter cluster smaller than | 3 |
| output name | |
| figure height | 5 |
| figure width | 9 |
| survival legend position | OUT |
| pvalue cutoff | 1 |
| qvalue cutoff | 0.25 |
| make figure | ONLYSIG |
| nozzle ver | Nozzle.R1 |
| options | MUTSIG |
| report title | |
| job description |
| Output Files: | |
| table.1.txt | |
| nozzle.RData | |
| nozzle.html | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 23:01:56 05-08-12 |
| Completed: | 23:03:50 05-08-12 |
| Elapsed: | 00 hrs 01 mins 54 secs |