RNA-Seq Analysis

Expertise

HPCBio analysts have extensive experience performing RNA-Seq analyses, including:

1. Consultation about experimental design and analyses
2. Data processing using best-practice workflows and quality control checks
3. Differential gene/transcript expression analysis 
4. Whole Gene Coexpression Network Analysis (WGCNA)
5. Gene set enrichment analysis (GSEA) and pathway analyses (KEGG, GO, etc)
6. Publication quality figure generation
7. Custom downstream analyses as needed by the client

We also have background working on a wide range of organisms and experimental designs, with data from multiple sequence-based and probe-based platforms. We utilize common, easily publishable open-source tools such as Salmon, STAR, and libraries for data analyses within the Bioconductor suite of R libraries. 

Please, contact us to discuss how we can be of assistance in achieving your project goals or to receive a quote for your project.

General Overview of RNA-Seq Workflow

RNA-Seq analysis includes genome alignment or mapping or pseudoalignment of reads to predicted transcripts, followed by generation of gene and transcript counts, and quality assessment of data. Initial expression analysis includes evaluation of read fates to assess how many reads mapped within annotated gene or transcript regions, followed by generation of a list of differentially expressed genes between experimental groups of interested.