Question: How to perform GISTIC analysis on GenePattern?
0
gravatar for Dmitri Ivanovich
4 weeks ago by
Dmitri Ivanovich0 wrote:

Hi guys, I have got a CNV data from TCGA and the marker file as shown below,

  • Seg file:
  • Sample Chromosome Start End Num_Probes Segment_Mean

  • TCGA.05.4249.01A 1 3218610 120527361 67456 -0.1725

  • TCGA.05.4249.01A 1 149881398 167526508 10663 0.5859
  • TCGA.05.4249.01A 1 167526675 167526823 2 -1.1518
  • TCGA.05.4249.01A 1 167526972 247813706 50571 0.5816
  • TCGA.05.4249.01A 2 484222 242476062 130861 0.0585

  • Markers file:

  • Probe.Name Chromosome Start

  • CN_473963 1 61735
  • CN_473964 1 61808
  • CN_473965 1 61823
  • CN_477984 1 62152
  • CN_473981 1 62920
  • CN_473982 1 62937

And my goal is to perform GISTIC analysis with the GISTIC 2.0 module in GenePattern, but the result is always like this: "GISTIC version 2.0.23 GISTIC 2.0 input error detected: 76606 segment start or end positions in '/opt/gpcloud/gp_home/users/genye/uploads/tmp/run8835511072592266907.tmp/seg.file/1/biguoshu1.txt' do not match any markers in '/opt/gpcloud/gp_home/users/genye/uploads/tmp/run6032895478607754030.tmp/markers.file/2/markersMatrix.txt'. First bad position is 10:24732567 at line 33."

I have uploaded my files in .txt format and choose the GISTIC version 6.15.28 and Human_hg19.mat as the refgene file. All other parameters were by default. Could anyone please tell me what the problem is and how to solve? Thank you !

cnv rna-seq tcga snp gistic • 129 views
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by Dmitri Ivanovich0

Follow up on this part of the error:

First bad position is 10:24732567 at line 33.

As it alludes to chromosome 10, perhaps one of your files is not sorted numerically, and is instead sorted lexicographically

ADD REPLYlink written 4 weeks ago by Kevin Blighe50k

Thank you for you helping Kevin! But after I sorted my files numerically, it still showed similar result (... do not match any markers...) . Is it possible that the Marker File I submitted doesn't fit TCGA data, or that the online version of GISTIC2 doesn't work at all?

ADD REPLYlink written 27 days ago by Dmitri Ivanovich0
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