RNA-seq data were deduplicated using PRINSEQ and trimmed using Trimmomatic. Differential expression between tissues was examined by aligning reads to the genome using TopHat and featureCounts relative to Trinity/Augustus transcripts. Statistical significance was assessed using fitNbinomGLMs in DESeq. Analysis of the experimental infection experiment was carried out using the CLC Genomics Workbench using read pairs mapped with a length fraction of 0.7 and a similarity fraction of 0.9 to annotate Trinity/Augustus transcripts. The Expectation-Maximization (EM) estimation algorithm of the suite was used to iteratively estimate the abundance of transcripts and assign reads to transcripts according to these estimates. The differential expression between experimental conditions was assessed with an assumption of a negative binomial distribution for expression levels and a separate generalized linear model for each mRNA, including a dispersion parameter, as is implemented in the edgeR package.

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