Performing Quantitative RNA-seq

RNA-Seq has revolutionized the study of gene expression by providing highly accurate estimates of transcript abundances through high-sensitivity detection and high-throughput analysis. Bioinformatic analysis pipelines that use RNA-Seq data typically start with a read quality control step, followed by either alignment to a reference or assembling sequence reads into longer transcripts afresh. After that, transcript abundances are estimated with sequence read counting and statistical models, and differential expression between samples is assessed. There are many technologies available for all steps of this pipeline. Quality control and read alignment will usually take place outside of R, so analysis in R will begin with a file containing transcript or gene annotations (such as GFF and BED files) and a file of aligned reads (such as BAM files).

The tools in R for performing analysis are powerful and flexible. Many of them are part of the Bioconductor...