Hi, i have got a CNV data from TCGA and i want to apply Gistic to extract the wide peaks and genes in each widee peak as well as cytoband?

Question

[Chaimaa]

i got the CNV data but i don(t know how to deal with it using GISTIC . the data format as follow:

Sample Chromosome Start End Num_Probes Segment_Mean

TCGA-3L-AA1B-10A-01D-A36Z-01 1 3208470 245880329 129047 0.0023

TCGA-3L-AA1B-10A-01D-A36Z-01 2 474222 217965694 116721 0.0074

TCGA-3L-AA1B-10A-01D-A36Z-01 2 217965888 217966775 2 -1.9301

TCGA-3L-AA1B-10A-01D-A36Z-01 2 217967898 242124735 14562 0.0115

TCGA-3L-AA1B-10A-01D-A36Z-01 3 526235 27449744 14708 0.0071

TCGA-3L-AA1B-10A-01D-A36Z-01 3 27470170 199023074 91656 5,00E-04

TCGA-3L-AA1B-10A-01D-A36Z-01 4 1043934 189836143 102727 6,00E-04

TCGA-3L-AA1B-10A-01D-A36Z-01 5 967233 107570801 56487 -6,00E-04

[WouterDeCoster]

What have you tried?

[Chaimaa]

I want to extract the genes in each region and discover the duplicated the deleted regions I want to apply GISTIC but i couldn't

[Chaimaa]

According to my knowledge Gistic2.0 can be used to analyze the copy number dataset (Level 3) for the identification of recurrent regions of copy number alteration and the copy number of genes. So, I want the list of genes in each region