This is the ENCODE-DCC RNA-sequencing pipeline. The scope of the pipeline is to align reads, generate signal tracks, and quantify genes and isoforms. RNA-seq data is valuable as it allows the measure of RNA expression levels as a transcriptional readout and the study of RNA structures in order to understand how RNA-based mechanisms impact gene regulation and thus disease and phenotypic variation. Since RNA populations are diverse, the ENCODE Consortium has developed the following RNA-seq pipelines: