Mapping TCGA hybridisation reference to sample barcode

Question

[Alexander Skates]

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?

Answer 1

[GenoMax]

See if either of these help.

sdrf from Broad: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/brca/cgcc/broad.mit.edu/genome_wide_snp_6/snp/broad.mit.edu_BRCA.Genome_Wide_SNP_6.mage-tab.1.2023.0/broad.mit.edu_BRCA.Genome_Wide_SNP_6.sdrf.txt

sdrf from UNC: https://tcga-data.nci.nih.gov/tcgafiles/ftp_auth/distro_ftpusers/anonymous/tumor/brca/cgcc/unc.edu/illuminahiseq_totalrnaseqv2/totalrnaseqv2/unc.edu_BRCA.IlluminaHiSeq_TotalRNASeqV2.mage-tab.1.1.0/unc.edu_BRCA.IlluminaHiSeq_TotalRNASeqV2.1.1.0.sdrf.txt

[Alexander Skates]

Yes, thank you!

[Shasha]

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?

[GenoMax]

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.