RNA-Seq Experiment and Data Analysis
With the ability to obtain tens of millions of reads, high-throughput messenger RNA sequencing (RNA-Seq) data offers the possibility of estimating abundance of isoforms and finding novel transcripts. In this chapter, we describe a protocol to construct an RNA-Seq library for sequencing on Illumina NGS platforms, and a computational pipeline to perform RNA-Seq data analysis. The protocols described in this chapter can be applied to the analysis of differential gene expression in control versus 17β-estradiol treatment of in vivo or in vitro systems.
Key wordsRNA-Seq Next-generation sequencing Data analysis Bioconductor Statistical analysis Differentially expressed genes
We thank Dr. Thomas Girke at the University of California Riverside for sharing his R scripts.
- 9.Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
- 10.R: A language and environment for statistical computing. http://www.r-project.org/