I didn't use the TCGA data website before, can someone please tell me how to download the CNV file for BRCA " breast cancer" from the TCGA data website.
Also what should the data look like? it should be .bed file
You can find a CNV file for each cancer patient here (around 1100).
For each patient there are 5 files (in the CNV column): The file "BRCA.focal_score_by_genes.txt" contain CNV scores for each gene in ALL BRCA samples. The 4 other files (all starting with "BRONZE") are two pairs of files: Two of them are with and without masked regions according to this. The two files for for each region appear to be different versions of the analysis (F9 vs F6) which I cannot find what the difference is. I would probably write and ask them.