Can I use virus expression value from VirusSeq?

Question

[oghzzang]

Dear Biostar users,

Hi.

I performed VirusSeq for detecting virus and virus integration sites from RNA-seq.

When I read this paper "Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq (Xiaoping Su et al, 2013 )", they counted expression level from viral transcript.

But, in VirusSeq package that they used, they didn't used expression level. They only used overall read counts.

How can I get virus expression value from VirusSeq output?

Thanks.