Hello everyone,
I am using GISTIC version 2.0.23 to analyse CNVs of nasopharyngeal carcinoma, and I get the CNVs of WGS and WES data by using control-freec. So I created an input file like this：
P20L 1 12081 14620 6 -0.153125626185084
P20L 1 14621 925886 92 -0.00685463283807697
P20L 1 925887 1182319 86 -1.20406685268504
P20L 1 1182320 1217509 12 -0.263116353239445
P20L 1 1217510 2556061 590 -0.13865279945587
P20L 1 2556062 3625678 154 -1.01911190070041
P20L 1 3625679 6519330 474 -0.147678291098717
And my command is displayed as follows: "gistic2 -b /disk/meimei/project/mNPC/CNV/GISTIC_results -seg /disk/meimei/project/mNPC/CNV/T_GISTIC_segmentation.txt -refgene /disk/soft/GISTIC_2_0_23/refgenefiles/hg38.UCSC.add_miR.160920.refgene.mat -genegistic 1 -broad 1 -armpeel 1 -savegene 1 -twoside 1"
However, I got an error information like this: "Setting Matlab MCR root to /disk/soft/GISTIC_2_0_23/MATLAB_Compiler_Runtime GISTIC version 2.0.23
GISTIC 2.0 input error detected: No copy number data detected."
Before I ran gistic with my samples, I have tested the software using the examplefiles and luckily can get the similar results of exampleresults. I wonder whether someone know the reason of this problem and how to deal with it?
Thank you for your attention, and I hope to receive you reply as soon as possible.
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written
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mm.beauty.lin •
3 answers
At last, I find the reason. Because there is one more tab at the end of the segmentation file, so that the software can't not recognize the content. When I remove the tab at the end of each line, I got the correct output.
Did u give header?
ID chrom loc.start loc.end num.mark seg.mean
Also try giving tab separated file.
If u can attach data for few sample, it can be traced for any error.
Hi, I am getting trouble in inputting control-freec output file into gistic. I always shows the error
GISTIC version 2.0.23 Warning: Number of markers is less than smooth length for the following chromosomes: 11. These chromosomes will not be smoothed. (Smooth length = 8.)
In smooth_cbs at 54
In clean_gistic_input at 77
In run_gistic2_from_seg at 238
In gp_gistic2_from_seg at 97
Index exceeds matrix dimensions.
Error in normalize_by_arm_length (line 85)
Error in make_sample_B (line 50)
Error in perform_deconstruction (line 68)
Do you know how to deal with it? THANK YOU
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tianshizuolu •
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Could you please provide details regarding how you generated this segmentation files for WES and WGS control freec data? I was wondering if you did a window based marker file , exon-level or something else? Thanks!
Here is information I've followed to generate the segmentation data and marker file: https://groups.google.com/a/broadinstitute.org/forum/#!searchin/gistic-forum/Whole$20Exome%7Csort:relevance/gistic-forum/BUjH7LF3T70/5rWlcPI5DAAJ . I wanted to clarify if you used the same method when doing a combined analysis of WGS and WES data.
Thanks!
Hello, I am also want to use control-Freec and GISTIC, but I don't know how to calculate the numer of markers in segement which was needed for GISTIC? How do you calculate that?