Question: How to download a list of cases containing specific cnvs from TCGA?
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gravatar for bsb4390
7 months ago by
bsb43900
bsb43900 wrote:

I am trying to obtain a list of all tcga cases for which there is a specific cnv (for example - brca2 gains). Using the GDC portal to access this data, I am able to get a list of all cases containing cnv's related to brca2, but I am unable to split this list into cases for which there is brca2 gain vs brca2 loss.

Does anyone know how to do this?

cnv tcga • 230 views
ADD COMMENTlink modified 7 months ago by Kevin Blighe45k • written 7 months ago by bsb43900
0
gravatar for Kevin Blighe
7 months ago by
Kevin Blighe45k
Kevin Blighe45k wrote:

The TCGA copy number data is arguably the most annoying because it has been processed and re-processed and made available on multiple domains across the World Wide Web. My 'go to' TCGA copy number data is that of the Broad Institute, which was processed by GISTIC 2.0. I give details of the link to this resource, here: C: How to extract the list of genes from TCGA CNV data

Once you download it, you can easily annotate it by following my code here: A: How to extract the list of genes from TCGA CNV data

I this way, you can have a reference dataset of somatic copy number gains/losses in all genes in all samples.

Kevin

ADD COMMENTlink written 7 months ago by Kevin Blighe45k
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