Question: Gistic input error : No copy number data detected
gravatar for
15 months ago by wrote:

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.

genome • 1.0k views
ADD COMMENTlink modified 11 months ago by tianshizuolu0 • written 15 months ago by

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!

ADD REPLYlink written 8 months ago by 29aprilkrutika10

Here is information I've followed to generate the segmentation data and marker file:!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.


ADD REPLYlink modified 8 months ago • written 8 months ago by 29aprilkrutika10

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?

ADD REPLYlink written 4 weeks ago by elainejihuihui0
gravatar for
13 months ago by wrote:

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.

ADD COMMENTlink written 13 months ago by
gravatar for pbpanigrahi
15 months ago by
pbpanigrahi180 wrote:

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.

ADD COMMENTlink written 15 months ago by pbpanigrahi180
gravatar for tianshizuolu
11 months ago by
tianshizuolu0 wrote:

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

ADD COMMENTlink modified 11 months ago by WouterDeCoster36k • written 11 months ago by tianshizuolu0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1296 users visited in the last hour