Question: How to query and download the WGS and gene expression data from paired solid Normal and solid Tumor samples in TCGA database?
gravatar for lazyplant
4.1 years ago by
lazyplant20 wrote:

I think this might be an easy question for some people, But I have stuck on this problem for a whole day. I need to download whole genome sequencing and gene expression data(counts of reads at each genes) from matched normal tissue and tumor tissue of the same patient. such as this figure in my dropbox.

I pocked around at GDC legacy Archive and can not figure out what are the relations among the files in a same case. I think I need more time to familiar with GDC data structure. Thanks!

gdc tcga • 1.8k views
ADD COMMENTlink modified 4.1 years ago by pxf10910 • written 4.1 years ago by lazyplant20

Have you tried

ADD REPLYlink written 4.1 years ago by fanli.gcb710

You may want to have a look at this answer to a very similar question that I asked.

ADD REPLYlink written 4.0 years ago by fr150
gravatar for pxf109
4.1 years ago by
pxf10910 wrote:

The TCGAbiolinks is a very useful tool for you. You can absolutely get the gene expression data through that. I am not sure whether you can get whole genome data, some data is not open for everyone.

ADD COMMENTlink written 4.1 years ago by pxf10910
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