I am not understanding how to download a full matrix of a TCGA subset (e.g. Colon Adenocarcinoma).
I selected Download Data > Data matrix > COAD Data matrix but I am getting a lot of files (level 3).
I want only the matrix of genes x samples. Have I to assemble it or can I download it somewhere?
Thanks Sebastian, I got it. Just a little question: is there a reason why I have to select RNA-Seq and not RNA-SeqV2 or TotalRNA-SeqV2?
Sorry for the late reply. That is actually a very good question. The differences between RNA-Seq and RNA-SeqV2 e.g. is a different (computational) processing to determine expression levels (e.g. RSEM instead of RPKM) => https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2
So, as far as I understand the (raw) sequencing data is the same (which you can only access when you succesfully applied for access), but the processing differs.
I would recommend UCSC Xena. The same team developed Xena and Cancer Browser mentioned above. The last data release on the UCSC Cancer Genomics Browser is Feb 2015. Since then, all new data are only being released from our team to Xena at http://xena.ucsc.edu . Drill down to the cohort of your interest, and then dataset of your interest, click the download button on the dataset detail page for bulk download.
For example: the COAD (colon cancer, TCGA) RNAseq gene expression estimation dataset page is at this url:
Hope this is helpful.
There doesn't seem to be a "download button" anymore as you mentioned. Nor does the link work - but this is 3yrs old, so I'm not surprised.
There is a download link .once you select your interested cancer dataset and choose the study(for eg:htseq count). There u find download link on the top.