Question

HTSeq Counts no longer available

3

Entering edit mode

vm ▴ 30

@vm-21340

Last seen 22 months ago

Brazil

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?

TCGAbiolinks • 3.4k views

ADD COMMENT • link updated 2.5 years ago by swbarnes2 ★ 1.4k • written 2.7 years ago by vm ▴ 30

0

Entering edit mode

j.arizanova • 0

@jarizanova19-23058

Last seen 2.5 years ago

United Kingdom

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?

ADD COMMENT • link 2.5 years ago j.arizanova • 0

0

Entering edit mode

STAR's output was intended to mimic HTseq-counts.

ADD REPLY • link 2.5 years ago swbarnes2 ★ 1.4k

score 2 · Accepted Answer · 2022-04-01

2

Entering edit mode

Benedek ▴ 20

@4a8e28bb

Last seen 2.5 years ago

Germany

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.