RNA-seqBioinformatics Tools
In recent years, RNA-seq has emerged as a powerful technology in estimation of gene or transcript expression. ‘Union-exon’ and transcript based approaches are widely used in gene quantification.
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Figure 1: Illustration of different gene quantification methods. A) A hypothetical gene, its two isoforms and read coverage profile. Assuming that the sum of mapped reads from all genes is 1 million, and each small and large exon is 1 kb and 2 kb long, respectively. B) ‘Union-exon’ based approach. After exon flattening, the ‘union exons’ are 2 kb, 1 kb and 2 kb long, respectively. The calculated RPKM is 6.4. C) transcript-based approach. Mapped reads are first assigned to individual isoforms, and the corresponding expressions for the two isoforms are 2 RPKM and 6 RPKM, respectively. In this calculation, the entire gene expression is 8 RPKM.