Copy Number Variation Analysis using GISTIC - Tutorial

[@yiqingzhang-wv7uu]

The following error has been reported when using gistic online analysis. How can I solve it? 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) Error in perform_ziggurat_deconstruction (line 126) Error in run_focal_gistic (line 151) Error in run_gistic20 (line 124) Error in run_gistic2_from_seg (line 249) Error in gp_gistic2_from_seg (line 97) MATLAB:badsubscript

[@FarhanHaqj]

Check these lines in the segment file

[@hanieazari4251]

dear farhanq thanks a lot for your tutorial on GISTIC, I used this protocol to analyse TCGA COAD cnv, however I faced this error " shortened 60segments in ... that overlap by one marker" how should i resolve this issue?

[@FarhanHaqj]

Did you make the markers file yourself?

[@hanieazari4251]

dear farhan, should I prepare any marker file? can I download it from TCGA? Also I have another question, my amp/del plot for another dataset is very noisy, should I filter CNV file before runining GISTIC? or any normalization such az RNAseq analysis? I really nead your response, Ive been searching all the week with no progress 🙏

[@FarhanHaqj]

@@hanieazari4251 ​ I would suggest you to go to cbioportal. Search for your dataset of interest. Download all the files of the data. You can find a data_cna.seg file in those files and run that on GISTIC.

[@FarhanHaqj]

how to download data from cbioportal and access is available on my channel.

[@hanieazari4251]

tnx a lot 🙏🙏

[@grayneo]

Thank you so much. This really helped me a lot.

[@FarhanHaqj]

Pleasure

[@veerpalbrar1155]

Please suggest me some topics for research and I want to do ph d computer engineering (bioinformatics field)

[@veerpalbrar1155]

Please help me for choosing research topic in bioinformatics computer science field

[@leilakamkar310]

Great tutorial. Thanks!

[@FarhanHaqj]

Pleasure

[@yujuahn7025]

It was very helpful! I really needed this tutorial. Thank you very much :)

[@FarhanHaqj]

Pleasure

[@yujuahn7025]

@@FarhanHaqj I downloaded copy number variation data from TCGA (gene_level_copy_number). But as this looks different to the segmentation file for the input of GISTIC, I am not too sure how I can alter the file I downloaded from the TCGA website. Can I please ask you about this?

[@pargenlab2463]

Thanks for the tutorial.

[@v.2435]

Thanks for the tutorial. Just wondering how the threshold is derived for assigning the copy number (-2,-1,0,1,+2)

[@FarhanHaqj]

-1 -2 is for hetero/Homo deletions while 1 2 is for gain and high copy gain The threshold are set in the beginning. You can check the parameters.

[@v.2435]

@@FarhanHaqj Thank a lot.

[@ramitasharma1524]

sir , can i have your email id ?