TCGA has recently migrated to the Genomic Data Commons (GDC). Following this migration, many tools convenient for retrieving TCGA data, such as TCGA-Assembler, no longer apply. So, with the new GDC, I'd like to download RNA-Seq data (in bulk) for tumor samples as well as normal control samples. How might I accomplish this?

I know how to download data from the GDC, but I need to know whether a specific RNA-seq data file is coming from a tumor how to obtain its "matched normal tissue" RNA-seq data. I'd like to do this in bulk, for, say, the HCC project.

I know there's a "legacy portal" for the old TCGA data on the GDC website, but I want to use the newest GDC portal.

Thanks in advance.
Hi everyone,

After looking around, it seems that a few people are having similar problems. So, I contacted GDC and they responded very quickly and helped me find a solution, which I'm posting here in hopes that it well help someone in the future :)

Here's how you do it:

1) Select all the files you want to download, and get the manifest file

2) Use the GDC api (documented here: https://gdc-docs.nci.nih.gov/) as follows: Use the "filters" parameter to get only files with files.file_id matching the UUIDs of the files you want to download (those UUIDs are the first column of the manifest file). Use the "fields" parameter, and set it to "file_id,file_name,cases.submitter_id,cases.samples.sample_type" -- this will get you the file name, the patient (i.e. cases.submitter_id), and what type of sample is it (tumor, normal, etc.)

Here's some quick code (which the person at the GDC help center was kind enough to provide):

 

     {
    	"filters":{
    		"op":"in",
    		"content":{
    			"field":"files.file_id",
    			"value":[
    				"9c5e4668-5ed8-4d7e-972a-6e985b0030df",
    				"629fb40f-e97d-4bb8-8f59-0a71256211b1"
    			]
    		}
    	},
    	"format":"TSV",
    	"fields":"file_id,file_name,cases.submitter_id,cases.samples.sample_type",
    	"size":"100000"
    }

Replace UUIDs with the UUIDs that you're interested in. With some basic shell and JSON, it should be pretty straightforward :)