Question: Cbioportal/Tcga Cnv Data
1
gravatar for RoyC
7.0 years ago by
RoyC150
Penn State University
RoyC150 wrote:

Does anyone know where to download gistic_amp_file or gistic_del_file as well as the case_file from CBioPortal or TCGA?

Thank you!

copynumber tcga cnv • 3.5k views
ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 7.0 years ago by RoyC150
3
gravatar for B. Arman Aksoy
7.0 years ago by
B. Arman Aksoy1.2k
New York, NY
B. Arman Aksoy1.2k wrote:

cBioPortal imports those files automatically from the latest run of Broad's Firehose: http://gdac.broadinstitute.org/runs/

From there, it is really easy to get those files, for example: http://gdac.broadinstitute.org/runs/analyses__2013_09_23/data/GBM/20130923/gdac.broadinstitute.org_GBM-TP.CopyNumber_Gistic2.Level_4.2013092300.0.0.tar.gz

Or simply, you can use firehose_get tool to download them in batches: https://confluence.broadinstitute.org/display/GDAC/Download

ADD COMMENTlink written 7.0 years ago by B. Arman Aksoy1.2k
1
gravatar for Charles Warden
7.0 years ago by
Charles Warden7.9k
Duarte, CA
Charles Warden7.9k wrote:

I would usually download copy number data from the HTTP FTP:

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/

For example, here is where you can find copy number calls for colon cancer samples (COAD) from Affy SNP arrays:

https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/coad/cgcc/broad.mit.edu/genome_wide_snp_6/snp/

It is a bit confusing because the publicly available data contains copy number and not SNP calls.

You may be able to get access to more data with special permission. For example, the files are not labeled as you describe above. See below for access information:

https://tcga-data.nci.nih.gov/tcga/tcgaAccessTiers.jsp

ADD COMMENTlink written 7.0 years ago by Charles Warden7.9k
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