ABSTRACT
Application of standard RNA sequencing (RNA-seq) protocols to virus-infected cells automatically yields reads from both host and virus transcripts (previously termed dual RNA-seq). This allows simultaneously profiling host and virus transcription in the same experiment. This chapter provides an overview on bioinformatics analysis of dual RNA-seq data and the challenges that arise when extending standard RNA-seq analysis pipelines to these data. These challenges include the parallel mapping of reads to host and viral genomes and problems due to incomplete annotations of viral genomes; normalization of gene expression changes to account for global changes in transcription or RNA stability in virus infected cells; and potential pitfalls for interpreting results from standard analyses due to unforeseen novel mechanisms being at play during virus infection.
