Question: How to link TCGA/GDC HTSeq or FPKM data with clinical data?
gravatar for ddzhangzz
18 months ago by
United States
ddzhangzz60 wrote:

I retrieved FPKM-UQ data (disease=GBM) from TCGA/GDC data portal and am wondering how to link the data with clinical data. The manifest file was looking like this:

 id filename    md5 size    state
000e76af-9529-4e0b-b300-c602f5f717d2    b836a8d2-7c37-4af5-9f2f-7bf0121717f9.FPKM-UQ.txt.gz 9e947e256131eee23678eb4e37a25c39    529524  submitted

And the corresponding FPKM-UP data for this sample will such like as:

ENSG00000242268.2   8781.02575294
ENSG00000270112.3   1003.38428979
ENSG00000167578.15  93710.2818553
ENSG00000273842.1   0.0
ENSG00000078237.5   64054.6191797
ENSG00000146083.10  225290.530508
ENSG00000225275.4   0.0
ENSG00000158486.12  24.5145025346
ENSG00000198242.12  1940563.1594
ENSG00000259883.1   3329.64812635

For clinical data I have another manifest file such as:

id  filename    md5 size    state
b32f2848-6ed2-4ce0-917c-ef9179c65b88    b32f2848-6ed2-4ce0-917c-ef9179c65b88/nationwidechildrens.org_clinical.TCGA-32-4208.xml  3b1c544c30fbc7cf11ef78b0322e53bb    45799   live

The clinical data usually have bcr-patient_uuid but how to link FPQM-UQ data by which the clinical data from.

rna-seq • 1.3k views
ADD COMMENTlink modified 15 months ago by Smandape60 • written 18 months ago by ddzhangzz60
gravatar for Smandape
15 months ago by
United States
Smandape60 wrote:

There is a similar thread, here, that mentions how to map UUIDs to TCGA barcode might answer your question.

ADD COMMENTlink written 15 months ago by Smandape60
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