Question: How To Get Gistic Or Rae Copy Number Variance Data Files For Copy Number Variance From Either Tcga Or Cbioportal?
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gravatar for RoyC
5.4 years ago by
RoyC140
Penn State University
RoyC140 wrote:

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!

tcga cnv • 5.2k views
ADD COMMENTlink modified 5.4 years ago by B. Arman Aksoy1.2k • written 5.4 years ago by RoyC140
0
gravatar for Charles Warden
5.4 years ago by
Charles Warden6.9k
Duarte, CA
Charles Warden6.9k wrote:

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

ADD COMMENTlink written 5.4 years ago by Charles Warden6.9k
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gravatar for B. Arman Aksoy
5.4 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

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/

ADD COMMENTlink written 5.4 years ago by B. Arman Aksoy1.2k
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