How to get RNA-Seq raw counts of primary tumor samples from TCGA patients with a certain gene mutated?

Question

[dagsbio]

Dear all,

I am struggling to find an easy way to get RNA-Seq raw counts of primary tumor samples from TCGA patients with a certain gene mutated.

I have tried few R scripts posted in biostars but I haven't figured out the way to adress this question, besides when trying to go through https://portal.gdc.cancer.gov/ I always end up downloading blood derived normals too that then I need to filter out one by one as I haven't found a "bioinformatic" way to do it yet...any suggestions?

Thank you!

Answer 1

[dagsbio]

Just found an easy way to get rid of non-tumor samples here: TCGA BRCA Solid Tissue Normal Filter