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.