TCGAbiolinks HT-Seq count

Question

[Elizabeth]

Hi everyone!

For legacy = F data, does workflow_type = HTSeq counts still work?

This is my code and it fails:

query <- GDCquery(project = "TCGA-BRCA",
                  legacy = FALSE,
                  data.category = "Transcriptome Profiling",
                  data.type = "Gene Expression Quantification",
                  workflow.type="HTSeq - Counts",
                  sample.type = "Primary Tumor")

I want to download only the raw data for protein coding genes.

Thanks!

Answer 1

[pilargmarch]

From TCGAbiolinks Github issues page:

There is no more "HTSeq - Counts" in GDC just STAR-counts. For TCGA data, you should be using the unstranded assay.

The GDC release 32.0 of March 29, 2022 said this:

Files from the HTSeq pipeline are no longer supported and will no longer appear in the portal. Normalized counts can now be found in the STAR-Counts files.