Retrieving tumor only data from GDC (TCGA) data portal.
1
0
Entering edit mode
4.9 years ago
dr.dimo • 0

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 • 2.3k views
ADD COMMENT
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode
4.9 years ago
Mike ★ 1.7k

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 COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 2965 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6