| GetReducedSegments1 seglist | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LGG-TP/2328413/2.GDAC_MergeDataFiles.Finished/LGG-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt |
| GetReducedSegments1 by | gene |
| GetReducedSegments1 featurename | Hybridization.REF |
| GetReducedSegments1 imput | FALSE |
| GetReducedSegments1 XY | FALSE |
| GetReducedSegments1 what | median |
| GetReducedSegments1 outname | LGG-TP |
| GetReducedSegments1 segmentid | Sample |
| GetReducedSegments1 chromosome | Chromosome |
| GetReducedSegments1 start | Start |
| GetReducedSegments1 end | End |
| GetReducedSegments1 segmean | Segment_Mean |
| Execution Times: | |
| Submitted: | 16:14:54 23-01-13 |
| Completed: | |
| Elapsed: | 06 hrs 38 mins 41 secs |
step 1. GetReducedSegments [id: 299313] Taking a copy number level 3 data and then converting it to a gene by sample matrix
urn:lsid:broadinstitute.org:cancer.genome.analysis:00240:28
| seglist | file:/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_MergeDataFilesPipeline/LGG-TP/2328413/2.GDAC_MergeDataFiles.Finished/LGG-TP.snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg.seg.txt |
| by | gene |
| featurename | Hybridization.REF |
| imput | FALSE |
| XY | FALSE |
| what | median |
| outname | LGG-TP |
| segmentid | Sample |
| chromosome | Chromosome |
| start | Start |
| end | End |
| segmean | Segment_Mean |
| Output Files: | |
| LGG-TP.RS.tsv | |
| .lsf.out | |
| stdout.txt | |
| Execution Times: | |
| Submitted: | 16:15:01 23-01-13 |
| Completed: | 22:53:34 23-01-13 |
| Elapsed: | 06 hrs 38 mins 33 secs |