Question: TCGA COAD and READ annotations missing from GDC commons?
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gravatar for ckr123
2.7 years ago by
ckr12310
Houston
ckr12310 wrote:

I used to download data from the old TCGA annotations manager to identify DNU cases, but I could not find it in the either the GDC data portal or GDC Legacy Archive. Any suggestion?

tcga • 1.1k views
ADD COMMENTlink modified 2.7 years ago by igor8.7k • written 2.7 years ago by ckr12310

Such annotation still exist in GDC as "annotation" nodes in the GDC Database, and queryable using APIs. As all metadata in GDC are maintained in a single Graph Database and accessible by API (and UI), there are no separate "annotation database" or "annotation manager" in GDC.

ADD REPLYlink written 9 months ago by Zhenyu Zhang260
1
gravatar for igor
2.7 years ago by
igor8.7k
United States
igor8.7k wrote:

Some alternatives:

For some reason, some of the data didn't port over to GDC from the old TCGA portal.

I had a similar question earlier: Why is TCGA Genomic Data Commons missing some data?

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by igor8.7k

Thank you, igor! I will email GDC support as well to see how they were doing on porting old data.

ADD REPLYlink written 2.7 years ago by ckr12310
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