Whole Transcriptome Sequencing (WTS) gives a complete RNA view, capturing isoforms, splicing, non-coding RNAs, and complex transcript structures. It’s ideal for deep mechanistic insights.
3′ mRNA-Seq is ideal for streamlined, cost-efficient gene expression quantification. It requires lower sequencing depth, simplified data analysis, and works exceptionally well with degraded or FFPE samples.
Despite differences, both methods deliver highly comparable pathway-level conclusions — making the right choice a matter of scope, sample type, and budget.