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Downloading epigenetic and mutation data of specific TCGA BRCA samples

I am working on cancer genomics. I downloaded TCGA BRCA FPKM data for my analysis. after some preliminary analysis, I categorised 250 samples in total 2 distinct categories. Now I want to analyse and compare their epigenetic and mutation patterns. After downloading all mutation and epigenetic data from TCGA BRCA, none of the samples from my previous analysis is matching. Suppose, TCGA-AN-A0AK-01A-21R-A00Z-07 sample is present in my previously downloaded FPKM data. But TCGA-AN-A0AK-01A-21W-A019-09 is available in the mutation data. Are these ids the same? For FPKM data and mutation data, do the same sample (individual) be represented by different Ids? Please help me, Thank you in advance.

mutation rna-seq tcga
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updated by aUser • aUser • written by Soura • Soura

1 answer

Hi, you might have solve the problem, but for the future reference, I am writing this. The nomenclature of TCGA data set is explained here:

https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/

To match a sample, you need to compare the first 4 parts of the barcode "TCGA-AN-A0AK-01A", the remaining part represent aliquot and the type of analysis, RNA-seq, DNA-sq, methylation or metabolites etc.

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written by aUser • aUser

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