| mutsig2cluster_new1 sample gene table file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/MergeMutSigRunResults/COADREAD-TP/4479003/COADREAD-TP.sample_sig_gene_table.txt |
| Correlate_Cluster_mutation_onlysig2 clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/COADREAD-TP/4432153/COADREAD-TP.transferedmergedcluster.txt |
| Correlate_Cluster_mutation_onlysig2 filter cluster smaller than | 3 |
| Correlate_Cluster_mutation_onlysig2 output name | COADREAD-TP |
| Correlate_Cluster_mutation_onlysig2 figure height | 5 |
| Correlate_Cluster_mutation_onlysig2 figure width | 9 |
| Correlate_Cluster_mutation_onlysig2 survival legend position | OUT |
| Correlate_Cluster_mutation_onlysig2 pvalue cutoff | 0.05 |
| Correlate_Cluster_mutation_onlysig2 qvalue cutoff | 0.25 |
| Correlate_Cluster_mutation_onlysig2 make figure | ONLYSIG |
| Correlate_Cluster_mutation_onlysig2 nozzle ver | Nozzle.R1 |
| Execution Times: | |
| Submitted: | 02:30:27 05-10-13 |
| Completed: | |
| Elapsed: | 03 hrs 27 mins 39 secs |
step 1. mutsig2cluster_new [id: 480779] 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/MergeMutSigRunResults/COADREAD-TP/4479003/COADREAD-TP.sample_sig_gene_table.txt |
| maf file | |
| sig gene file | |
| sig gene q cutoff | 0.01 |
| output name |
| Output Files: | |
| COADREAD-TP.mutsig.cluster.txt | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 02:30:27 05-10-13 |
| Completed: | 05:57:21 05-10-13 |
| Elapsed: | 03 hrs 26 mins 54 secs |
step 2. Correlate_Cluster_mutation_onlysig [id: 480780]
urn:lsid:broadinstitute.org:cancer.genome.analysis:00503:3
| cluster label file | COADREAD-TP.mutsig.cluster.txt |
| clinical info file | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering_new/COADREAD-TP/4432153/COADREAD-TP.transferedmergedcluster.txt |
| features used | ALL |
| filter cluster smaller than | 3 |
| output name | COADREAD-TP |
| figure height | 5 |
| figure width | 9 |
| survival legend position | OUT |
| pvalue cutoff | 0.05 |
| qvalue cutoff | 0.25 |
| make figure | ONLYSIG |
| nozzle ver | Nozzle.R1 |
| options | MUTSIG |
| report title | |
| job description |
| Execution Times: | |
| Submitted: | 02:30:27 05-10-13 |
| Completed: | 05:58:06 05-10-13 |
| Elapsed: | 03 hrs 27 mins 38 secs |