Our bioinformatics department has developed state-of-the-art RNA-Seq analysis pipelines which follow a reference-based or de novo approach. The ultimate goal is to provide our customers with the best possible answers to their transcriptome analysis research questions. To accomplish this task we generally use the Illumina HiSeq sequencing platform. If no annotated reference genome is available, we are able to generate high-quality de novo transcriptome assemblies with Trinity (Grabherr et al., 2011), and subsequently annotate transcripts using our in-house annotation pipeline. Based on an annotated reference genome and mRNA sequencing reads, gene expression levels are calculated using a combination of Bowtie2/Tophat2 and cufflinks based on the work of Trapnell et al (2013).
Quality control and statistical interpretation
Our standard service also includes a number of quality control steps based on the overall distribution of gene expression in the samples. These steps result in publication-ready figures such as a principle component analysis (PCA) scatter plot and a hierarchical clustering figure to inspect inter- and intra-group variability.