TCGA dataset has 2 HTSeq readcounts file for same tisssue

Question

[MatthewP]

I download TCGA-BLCA HTSeq readcounts file and find some samples have 2 files. Like:

$grep TCGA-BL-A0C8-01A gdc_sample_sheet.2019-09-10.tsv
f832dfd0-f52e-4835-8ae1-144a171e922f    d4be1d22-3ece-42e9-9d92-0fdb3dc95c3a.htseq.counts.gz     
Transcriptome Profiling Gene Expression Quantification  TCGA-BLCA   TCGA-BL-A0C8    TCGA-BL-A0C8-01A    Primary Tumor
20976445-b2a0-45ad-a89a-9273938727c6    b142177f-f89e-4e5a-834b-a75e7ab0b618.htseq.counts.gz     
Transcriptome Profiling Gene Expression Quantification  TCGA-BLCA   TCGA-BL-A0C8    TCGA-BL-A0C8-01A    Primary Tumor

Which one should I use for downstream analysis?

Answer 1

[yasokannan93]

A similar post: Samples with same TCGA barcode in TCGA data

Based on the approach here, you can use aliquot with later plate number. You will have to get the full TCGA barcode for this sample and choose one.

To know about the TCGA codes:

https://docs.gdc.cancer.gov/Encyclopedia/pages/TCGA_Barcode/ https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/sample-type-codes