Figure 1.

Pipeline flow chart. Flow chart depicting the steps in the pipeline and two main use cases. (a) expression estimation using a pre-defined transcriptome reference; (b) construction of a custom transcriptome reference from the data followed by expression estimation. Haplotype-specific expression can be obtained using a pre-defined transcript reference if the parental transcriptome sequences are known and recombination has no effect (for example in the case of an F₁ cross of two inbred strains). If the standard (for example Ensembl) reference is used, then isoform-level estimates are produced. If a custom reference is constructed solely to avoid allelic mapping biases, the phasing of genotypes can be omitted and isoform-level estimates are produced. If the genotypes are phased, haplo-isoform estimation is performed.