Uncovering the Complexity of Transcriptomes with RNA-Seq

Figure 5

Mapping and quantification of the signal. RNA-seq experiments produce short reads sequenced from processed mRNAs. When a reference genome is available the reads can be mapped on it using efficient alignment software. Classical alignment tools will accurately map reads that fall within an exon, but they will fail to map spliced reads. To handle such problem suitable mappers, based either on junctions library or on more sophisticated approaches, need to be considered. After the mapping step annotated features can be quantified.