Question: Retrieving tumor only data from GDC (TCGA) data portal.
0
gravatar for dr.dimo
2.7 years ago by
dr.dimo0
dr.dimo0 wrote:

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.

gdc tcga • 1.5k views
ADD COMMENTlink modified 2.7 years ago by Mike1.3k • written 2.7 years ago by dr.dimo0

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

ADD REPLYlink written 2.7 years ago by zjhzwang180
1
gravatar for Mike
2.7 years ago by
Mike1.3k
UK
Mike1.3k wrote:

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)

ADD COMMENTlink written 2.7 years ago by Mike1.3k

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.

ADD REPLYlink written 2.7 years ago by dr.dimo0
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