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

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
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updated by Mike Mike • written by dr.dimo • dr.dimo

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

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written by zjhzwang zjhzwang

1 answer

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)

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written by Mike Mike

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.

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written by dr.dimo • dr.dimo

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