This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Mapping TCGA hybridisation reference to sample barcode

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, e.g., 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
• 4,613 views • link
updated by GenoMax GenoMax • written by Alexander Skates Alexander Skates

1 answer

enter image description here

Hi, when I clicked on the link it didn't download the file, but the TCGA URL popped up, what should I do to download the file?

• 0 views • link
written by Shasha • Shasha

TCGA data moved to the new GDC portal some time back: https://portal.gdc.cancer.gov/

Take a look there to see if you find the information you are looking for.

• 0 views • link
written by GenoMax GenoMax

Log in to answer this question.

More posts like this