CPTAC data, download, merge

Question

[Rob]

Hey friends

I downloaded RNA seq data of CPTAC from GDC portal. I want to merge them as one file.

I have my python script and manifest file in the same folder and I am running the following code in the command prompt to merge them. it gives me 3 folders :HTSeq - count; HTSeq - FPKM; HTSeq - FPKM-UQ; but they are empty. why is that?

python gdc-rnaseq-tool.py manifest_file.txt

Could you help me with this?

[Mohita]

I am also facing the same problem. I will be grateful if you help me out for this.

Answer 1

[Zhenyu Zhang]

This is because HTSeq count is no longer supported after Data Release 32. The tool finds zero files to aggregate from, so you end up with empty folders.