Question: Accessing legacy data in GDC
gravatar for fr
3.2 years ago by
fr130 wrote:

I am trying to retrieve legacy data from GDC through TCGAbiolinks. Specifically, I'd like to retrieve all RNAseq data for "CCLE-BLCA', which you can access through this link.

I ran

query <- GDCquery(project = "CCLE-BLCA", legacy = TRUE)

and got the full table with all project ids, name, etc. But I always get the error

Error in checkProjectInput(project) : Please set a valid project argument from the column project_id above. Project CCLE-BLCA was not found.

Are you aware of a way to download this data?

rna-seq R tcgabiolinks • 1.1k views
ADD COMMENTlink modified 2.7 years ago by Kevin Blighe63k • written 3.2 years ago by fr130
gravatar for Kevin Blighe
2.7 years ago by
Kevin Blighe63k
Kevin Blighe63k wrote:

Yes, on the GDC Legacy website, after you have filtered the project and samples that you want, download the file manifest and then use the GDC Data Transfer Tool, which will take the manifest as input, in order to download everything.

ADD COMMENTlink written 2.7 years ago by Kevin Blighe63k
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