Retrieving tumor only data from GDC (TCGA) data portal.

Question

[dr.dimo]

Greetings and salutations,

I am interesting in retrieving copy number segmented data from the data portal, but only from the primary tumor samples, is there a way to just select these as opposed to data from the matched normal?

Thanks in advance.

[zjhzwang]

You mean you can only get the tumor samples,and you want to get normal samples?

Answer 1

[Mike]

Have a look at following related post...

A: Protocol to Downlad TCGA data from GDC

A: Retrieving data from new data portal of tcga

or simply you can retrieve by Broad GDAC Firehose (https://gdac.broadinstitute.org/) or CGDS-R package ( cBioportal).

you can extract your desire sample based on TCGA sample barcode..

Tumor types range from 01 - 09, normal types from 10 - 19 and control samples from 20 - 29. (where -01 is for primary tumor)

[dr.dimo]

Thanking you for the reply, figured it out, you can select it from the "Samples Sample Type" within the "Add a Case/Biospecimen Filter" on the portal website.