Resolving host–pathogen interactions by dual RNA-seq
Fig 4
Bioinformatic analysis pipeline for dual RNA-seq datasets.
Quality-filtered RNA-seq reads are aligned in parallel against the respective host and pathogen replicons. Reads mapping equally well to both reference organisms (“cross-mappings”) are quantified and discarded from downstream analyses. Reads unequivocally mapped to either the bacterial or host reference are used for quantification and functional analyses. Dual RNA-seq enables a wide range of downstream analyses, discussed in detail in the text. “MT,” mitochondrial genome.