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Reading litterature about RNA-Seq on virus would be a good starting point.
This some kind of introduction (a review article from 2015) for fungy-viruses
https://www.sciencedirect.com/science/article/pii/S004268221500080X
https://ac.els-cdn.com/S004268221500080X/1-s2.0-S004268221500080X-main.pdf?_tid=6af0b17f-cdcf-41b0-ab2b-f811a4b166be&acdnat=1545437840_a95d0051bdebf0fa6d5a25d4130ec7a5 Look at their references, it should be useful
50-plus years of fungal viruses
They consider: Highlights • Historical perspective of fungal virus research. • Description, classification and diversity of fungal virus families. • Structural features of fungal virus particles. • Hypovirulence and exploitation of mycoviruses in biological control of plant pathogenic fungi.
There are very few articles about your topic.
I think I found another useful paper for you:
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1344-4
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts
Read it, it may be helpful.