Bioinformatics

Bioinformatics is the backbone of the RNomics Platform services. It includes basic experimental design and data analysis as well as client-specific meta-analysis. Bioinformatics is applied throughout most of our activities and is offered as part of standard service fees. For more in-depth or special requests, we offer a stand-alone consultation services on an hourly basis. Below are some examples of bioinformatics services available.

RNA-Seq analysis workflow

We offer a complete bioinformatics workflow to analyse RNA-Seq data from raw sequence to provide gene expression and alternative splicing event data sheets. The workflow is separated into three main stages: 1) cleanup, 2) alignment and quantification, and 3) expression data report (see Figure 3). The cleanup stage involves quality control such as read errors or duplications using FastQC, and adapter trimming using Trimmomatic. The alignment and quantification stage is the performing of read alignment to the transcriptome of interest (human, mouse, rat, or other available transcriptome sequence annotation) and computation of transcript expression using RSEM and Bowtie. With RSEM we obtain run-independent transcript abundance estimates, thus enabling both global gene expression and alternative splicing quantification. We provide complete data sheets containing expression data and statistical analyses such as Welch's t-test between groups of samples and false discovery rate controlled by q-value as well as unsupervised hierarchical clustering heatmaps.

Public RNA-Seq data analyses

Using the above worflow, we offer data analysis based on public RNA-Seq expression datasets, such as those provided by the National Cancer Institute Genomic Data Commons (formerly the Cancer Genome Atlas, or TCGA). The analysis workflow is analogous to our RNA-Seq workflow presented above. Clinical data can be integrated to perform statistical analyses based on different sample groups (e.g. stages, prognostic, age, etc.).