Question: TCGA Barcodes Missing from Bulk Data
1
gravatar for dirigible2012
4.5 years ago by
dirigible2012310
European Union
dirigible2012310 wrote:

I have downloaded the Level_3 data for CNV (SNP Array) for Breast Cancer from the Bulk Download section of TCGA.

The file names look like this:

MOHEL_p_TCGA_271_274_275_N_GenomeWideSNP_6_A01_1320320.hg18.seg.txt

The data in the "Sample" column within the file is the same.

I was expecting a barcode like "TCGA-A2-A0D0-01".

How do I match the data to the patient?

Thanks for helping,

Stephanie

barcodes tcga • 2.0k views
ADD COMMENTlink modified 4.4 years ago • written 4.5 years ago by dirigible2012310
4
gravatar for komal.rathi
4.5 years ago by
komal.rathi3.4k
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.4k wrote:

I think you should download the data using the Data Matrix. When you download the data, you automatically download files like FILE_SAMPLE_MAP.txt & file_manifest.txt. You will get the barcode along with the filename in these files. 

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by komal.rathi3.4k

Found it! Thanks.

ADD REPLYlink written 4.4 years ago by dirigible2012310

dirigible2012 if my answer helped you, then please accept it by clicking on the tick mark

ADD REPLYlink written 4.4 years ago by komal.rathi3.4k
0
gravatar for dirigible2012
4.4 years ago by
dirigible2012310
European Union
dirigible2012310 wrote:

Found the answer -

The Bulk Download appears to be mainly for downloading historic versions of the archives, and doesn't seem to provide file to barcode mapping.

The File Search tool is the answer for downloading the LATEST version of the archive. Each download will contain a "file_manifest.txt" file, which contains the filenames and barcodes for all files in the archive.  

ADD COMMENTlink written 4.4 years ago by dirigible2012310
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