Multiple Tumor Count Files from a single Patient. How to merge or select?

Question

[Rishav]

I was downloading RNA-SEQ Count files from the GDC Portal and I noticed a difference in the number of files and cases. Initially, I assumed the difference in files to be the normal files. However, even when that was accounted for there was still multiple tumor files that came from the same patient. How do I select which files to use for my analysis or is it possible for me to merge these files into singular files for analysis?

Answer 1

[Zhenyu Zhang]

Normally I won't merge them. As to which one to use, here is a list of things I will consider, in order

• sample type (primary vs metastasis)
• other omics data (if you are doing multi-omics, you'd like to use the ones on the same sample/analyte)
• data quality (coverage, percentage mapped, RIN)

[Rishav]

Thanks for the answer. We did find an old Broad Institute article on this and we ended up using that for our analysis