Forum:RNA seq data

Question

[doul_as]

I'd like please to know which software are very good and how to analyse mycoviruses ( fungal viruses) RNA-seq data in the purpose to report my results in a very good reputed sci journal.Thanks in advance

[Bastien Hervé]

Reading litterature about RNA-Seq on virus would be a good starting point.

[natasha.sernova]

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

Alison C TestaEmail author, James K Hane, Simon R Ellwood and Richard P Oliver

Read it, it may be helpful.