How To Get Gistic Or Rae Copy Number Variance Data Files For Copy Number Variance From Either Tcga Or Cbioportal?

Question

[RoyC]

Does anyone have any idea how can get GISTIC or RAE data files for copy number variance from either TCGA or CBioPortal? I want to use the data for MeMo runs; however, I can't seem to find the CNV data that match up with the format required for MeMo. Any help would be massively appreciated! Thank you!

Answer 1

[Charles Warden]

I haven't tried this particular tool, but it looks like it was designed with TCGA data in mind. What are the differences between the TCGA segmentation files you can download versus the input file in the example?

http://cbio.mskcc.org/wp-content/uploads/2012/10/MEMo_Readme.pdf

Answer 2

[B. Arman Aksoy]

You can download the GISTIC outputs from Broad Firehose's analyses runs, e.g.:

http://gdac.broadinstitute.org/runs/

or a better way would be to use the firehose_get tool:

https://confluence.broadinstitute.org/display/GDAC/Download

For example, to download GISTIC results for GBM, you would simply run this command:

firehose_get -o "GISTIC" analyses latest GBM

As far as I know, the RAE results are distributed as part of the first GBM paper in the supplementary material:

http://cbio.mskcc.org/cancergenomics/gbm/