Issues on GISTIC of GenePattern

[Dmitri Bi]

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:(For the affymetrix SNP6.0)

• 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_hg38.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 !

Job ID: 165784. GISTIC_2.0

   Server Platform: Mac

I met my problems in stdout.txt.

[Barbara Hill]

Hello Dmitri,

I'm so sorry that you've not received any help yet.

Are you still having difficulty with GISTIC in GenePattern?

We'll be happy to see what we can do to help.

Best

-Barbara