Hi @namarig
I just took a deep dive look at your data, and replied in your original thread. Let’s keep the conversation there.
In short, I think this is a scientific problem so far, not a technical problem. If you have other samples with the same scientific inputs (cross comparisons between a human tumor sample, and a virus), and some “work” and others don’t, that could be the data itself, or it could be a “result”.
Consolidating into Mirdeeper2 quantifier and Mirdeeper identication tools does not work(get errors - #4 by jennaj