| mutsig2cluster_new1 sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MutSigRun/SKCM-BRAF_Hotspot_Mutants/3156473/SKCM-BRAF_Hotspot_Mutants.sample_sig_gene_table.txt |
| Correlate_Clinical_Clusters_onlysig2 clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-BRAF_Hotspot_Mutants/3215664/SKCM-BRAF_Hotspot_Mutants.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: | 11:07:12 10-05-13 |
| Completed: | |
| Elapsed: | 00 hrs 03 mins 47 secs |
step 1. mutsig2cluster_new [id: 404310] 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/MutSigRun/SKCM-BRAF_Hotspot_Mutants/3156473/SKCM-BRAF_Hotspot_Mutants.sample_sig_gene_table.txt |
| maf file | |
| sig gene file | |
| sig gene q cutoff | 0.01 |
| output name |
| Output Files: | |
| SKCM-BRAF_Hotspot_Mutants.mutsig.cluster.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 11:07:14 10-05-13 |
| Completed: | 11:08:28 10-05-13 |
| Elapsed: | 00 hrs 01 mins 13 secs |
step 2. Correlate_Clinical_Clusters_onlysig [id: 404311]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00335:81
| cluster label file | SKCM-BRAF_Hotspot_Mutants.mutsig.cluster.txt |
| clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_clinicalDataPicker/SKCM-BRAF_Hotspot_Mutants/3215664/SKCM-BRAF_Hotspot_Mutants.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: | 11:07:14 10-05-13 |
| Completed: | 11:10:57 10-05-13 |
| Elapsed: | 00 hrs 03 mins 42 secs |