I want to download paired samples from the TCGA database of RNA-Seq experiments. I've been looking for information on how to download this data and it looks like it's from https://gdac.broadinstitute.org/. Specifically, I'm looking for breast cancer samples, so I looked in the mRNASeq section.
Inside this section there are several files to download (I want the raw counts) but I don't know what the differences are between the files:
illuminahiseq_rnaseqv2-RSEM_genes (MD5) illuminahiseq_rnaseq-gene_expression (MD5)
I would also like to know how to filter these files to keep the paired samples. I found something about the sample codes in a previous post, but I couldn't access the link to the explanation (https://wiki.nci.nih.gov/display/TCGA/TCGA+barcode).
Could you help me with this problem please?
PS: Suggestions about other databases are welcome!