Question: How to download TCGA normal sample ?
gravatar for najioumayma
8 weeks ago by
najioumayma10 wrote:

Hello. I want to do a differential analysis of gene expression and i need to have normal samples from the TCGA BRCA project. I tried to download it from GTEx data but i can't find samples with expression of my genes of interest. Is there a script to follow step by step to obtain this control data ?

rna-seq tcga R • 158 views
ADD COMMENTlink written 8 weeks ago by najioumayma10

See @Kevin's answer here : A: Low number of healthy samples in TCGA

TCGA project was conceived a long time ago when sequencing as still expensive. They decided to maximize the returns by prioritizing tumor samples.

You should be able to identify matched normals based on their ID's. In any case you will need to apply for access to original fastq data if that is what you are looking for.

ADD REPLYlink modified 8 weeks ago • written 8 weeks ago by GenoMax95k
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