Fig. 1

The workflow. We followed the primary steps in NGS transcriptome analysis (1: Generating raw reads, 2: Assembling reads, 3: Differential expression analysis and 4: characterization of differentially expressed genes) to understand the influence of non-target reads on transcriptome analysis. First, Liver cDNA of mice infected with the parasite S. mansoni (High dose infection: H, low dose infection: L and uninfected: U; 2 mice per group) were sequenced with Illumine HiSeq. Then, sixteen transcriptomes were assembled using both de novo (Trinity de novo and SOAPdenovo–Trans) and reference based (Genome guided Trinity and Cufflinks) approaches at the different infection levels, to identify the influence of parasite reads (i.e. xenobiotics) on transcriptome assembly. Subsequently, the transcriptomes were annotated and putative non-target transcripts were identified. Then differential expression was calculated, before and after filtering the transcripts of non-target origin, between infected and uninfected mice and between mice infected at different parasite loads. Finally after removing non-target reads from the transcriptomes the host gene expression corresponding to S. mansoni infection was characterized