Metatranscriptomic RNA-Seq Data Analysis of Virus-Infected Host Cells

RNA sequencing (RNA-seq)RNA sequencing (RNA-seq) analysis of virus-infected host cells enables researchers to study a wide range of phenomena involving host-virus interactions. This includes genomic analysis of the viral population itself, as well as analysis of the transcriptional dynamics of the virus and host during infection. In this chapter, we provide a guide for researchers interested in performing RNA-seqRNA sequencing (RNA-seq) data analysis of virus-infected host cells or cell lines. We outline several bioinformaticBioinformatics protocols for quantifying viral abundanceViral abundance, assembling viral genomes from mixed samples, and performing differential expression analysis, among other common workflows. These workflows can be used as starting points for researchers aiming to analyze RNA-seqRNA sequencing (RNA-seq) datasets of mixed samples containing both host and viral RNA, such as virus-infected cell lines or clinical samples.