Hello, everyone.

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!


In your file manifest that you used to download the data, you will have a UUID. Use that to look up the TCGA barcode for each file via this function: https://www.biostars.org/p/306400/#306517

You can then infer Tumour-Normal pairings by matching on the TCGA barcode. Yet more information on barcodes:

 - https://www.biostars.org/p/313063/#313066
 - https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables
 - https://github.com/kevinblighe/TCGAbarcode/blob/master/TCGAbarcode.pdf


I have already analysed the TCGA BRCA data many times and there are ~111 Tumour-Normal pairs for the RNA-seq data.

Kevin