Identification and quantification of gene isoforms during the differentiation of human embryonic stem cells into pharyngeal endoderm and primordial germ cell-like cells

Long-read RNA-seq is now widely applied for gene isoform identification and efforts to long-read RNA-seq for gene isoform quantification are emerging. We develop a software named miniQuant to quantify gene isoforms using long reads alone or in combination with short reads. We demonstrate the utility of miniQuant by its application in uncovering the expression dynamics of gene isoforms during the differentiation of human embryonic stem cells (ESC) into pharyngeal endoderm (PE) and primordial germ cell-like cells (PGC).