R Bioinformatics Cookbook

Performing Quantitative RNAseq

The technology of RNAseq has revolutionized the study of transcript abundances, bringing high-sensitivity detection and high-throughput analysis. Bioinformatic analysis pipelines using RNAseq data typically start with a read quality control step followed by either alignment to a reference or the assembly of sequence reads into longer transcripts de novo. After that, transcript abundances are estimated with read counting and statistical models and differential expression between samples is assessed. Naturally, there are many technologies available for all steps of this pipeline. The quality control and read alignment steps will usually take place outside of R, so analysis in R will begin with a file of transcript ...