Question: How to use TCGA miRNA seq data?
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gravatar for bhoomisharma04
5.2 years ago by
United States
bhoomisharma0410 wrote:

I have downloaded miRNA seq data for colon adenocarcinoma. As i am a beginner, i am facing difficulties to understand and interpret the data. I have miRNA seq files for all samples but how to find the file for the matched normal tissue? And how to study the expression of a particular miRNA across the whole sample set?

mirna seq tcga • 2.3k views
ADD COMMENTlink modified 5.1 years ago by Na Sed290 • written 5.2 years ago by bhoomisharma0410
1
gravatar for Na Sed
5.1 years ago by
Na Sed290
United States
Na Sed290 wrote:

When you download data from TCGA, it includes a text file, named "FILE_SAMPLE_MAP". In this file you can find the patient codes as well as corresponding file names.

If you seek matched normal/tumor samples, you must note to the barcode of patients. The 'participant' part of barcodes must be the same. For more information about TCGA barcodes, please see this.

ADD COMMENTlink written 5.1 years ago by Na Sed290

Sir, how to know whether a particular sample is healthy or cancerous? I just see expression data and no label. Where can I find it?

ADD REPLYlink written 4.2 years ago by acc.inpro32130

Please see the page that I have referred. In this page, as written, two digits in barcodes are "Sample". In the next table, it has been written that "Tumor types range from 01 - 09, normal types from 10 - 19 and control samples from 20 - 29."

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Na Sed290
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