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?