Question: download CNV file for breast cancer BRCA from TCGA website
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gravatar for mms140130
12 weeks ago by
mms14013050
mms14013050 wrote:

Hello,

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

Thank you,

gene • 224 views
ADD COMMENTlink modified 12 weeks ago by kristoffer.vittingseerup250 • written 12 weeks ago by mms14013050

There is not a "the" CNV file. There is a CNV file for each patient - so around 1100 according to this.

Is that what you want?

ADD REPLYlink written 12 weeks ago by kristoffer.vittingseerup250

Thanks for your answer, but there is 4 files for each patient which one is related to tumor ?

ADD REPLYlink written 12 weeks ago by mms14013050
2
gravatar for kristoffer.vittingseerup
12 weeks ago by
European Union
kristoffer.vittingseerup250 wrote:

You can find a CNV file for each cancer patient here (around 1100).

For each patient there are 4 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 (F10 vs F11) which I cannot find what the difference is. I would probably write and ask them.

ADD COMMENTlink written 12 weeks ago by kristoffer.vittingseerup250
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