Question: Mapping TCGA hybridisation reference to sample barcode
gravatar for Alexander Skates
4.2 years ago by
United Kingdom
Alexander Skates350 wrote:

I'm trying to carry out an eQTL analysis on some TCGA BRCA data I have.

For the genotypes, I have a list of birdseed files, that each have a hybridisation reference that looks like: WRIED_p_TCGA_143_147_150_Hahn_N_GenomeWideSNP_6_A09_799960.

My RNA-Seq data is labelled with a portion of the sample barcodes, eg: TCGA.3C.AAAU (which would correspond to the barcode TCGA-3C-AAAU-01A-11R-A41B-07).

For eQTL analysis, I need to pair up a genotype with the corresponding expression values, but I need a file providing the mappings. As per the TCGA Website, I feel like its probably a SDRF file I need, but I'm not entirely sure about this, and I can't find one through the TCGA data portal in any case.

Could someone lend me some guidance?

rna-seq genotype tcga • 2.1k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.2 years ago by Alexander Skates350
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