I'm working with breast cancer expression data from the TCGA-BRCA project. All my scripts were written to retrieve HTSeq counts from GDC, but they seem to have been removed from the GDC Data Portal. When using GDCquery, the only valid argument for "workflow.type" now seems to be "STAR - Counts". Is there a way to retrieve the older version HTSeq Counts?

Hi,

It seems that GDC got updated, this affects TCGAbiolinks as well (see GitHub issue). So I guess HTSeq counts are no longer available, only STAR counts.

Hi, can I ask a follow up question as I am facing exactly the same issue... The "STAR - Counts" workflow seems to generate augmented_star_gene_counts files - is any of the data in these files suitable for processing with edgeR?