special oligonucleotides or adapters to be attached to the surface of the appropriate sequencing platform. Then clonal amplification produces ~1,000 copies of a single member of the template library (i.e., copies, produced from a specific cDNA fragment); this set of copies is named a cluster. After cluster generation, the templates are sequenced by synthesis to obtain short sequences named targets or reads, which are typically 30-400 bp, depending on the technology used. As output, massively parallel sequencing produces tens of millions of reads, which describe the qualitative and quantitative composition of transcripts in the transcriptome. Following sequencing, the reads are either aligned to a reference genome or transcriptome to produce a large-scale transcription map that reveals the structure and abundance of the transcripts.
