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This step maps the aligned reads to transcripts using a modified E/M algorithm; detailed information about this algorithm can be found in the white paper RNA-Seq quantificationSeq quantification.

Given a list of transcripts, each read can be mapped to one of four classes: exonic, partially overlaps exon, intronic, or between genes (Figure 2). Generally, “exonic” means the read came from a sequence present in the mature mRNA, while “intronic” means the read overlaps a gene, but aligns to the portion of the sequence not present in the mature mRNA. Finally, “between genes” reads came from a region outside of any gene. Detailed definitions of all four types can be found below.

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