TCGA COAD and READ annotations missing from GDC commons?

Question

[ckr123]

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?

[Zhenyu Zhang]

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.

Answer 1

[igor]

Some alternatives:

• GDAC Firehose (all pre-2016 TCGA data): http://gdac.broadinstitute.org/runs/stddata__latest/
• ICGC Data Portal (includes some TCGA data): https://dcc.icgc.org/

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?

[ckr123]

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