The simple explanation is that they are different products that only overlap to a limited degree. If you're doing a standard RNA-seq experiment, short 100bp to

The simple explanation is that they are different products that only overlap to a limited degree. If you're doing a standard RNA-seq experiment, short 100bp to 200bp Illumina reads are just dandy for what you need. Most of the time, at least; you could, for example, be interested in different splice variants for a gene family; in that case longer continuous reads are valuable. But then it's no longer a standard RNA-seq. PacBio and pore-type sequencing is most valuable for polishing reference genome assemblies. For instance, this is a huge issue for crop plants because they have huge, repetitive genomes and are often polyploid. So there's a lot of interest in creating high quality assemblies not just for e.g. corn, but the major research inbreds (B73, Mo17, etc.) as well as private breeding lines. Some of the most valuable crop QTLs (R genes, microRNAs, transposon fragments, etc.) are just 'junk' sequence that plays a regulatory or defense role, so it's super important. In general, the Illumina data is very high quality and very inexpensive, and works beautifully provided you have a high-quality assembly to work with, and what you're interested in isn't very repetitive. It has many good applications, so I don't see much risk at this point. If, at some point, longer reads can be done with high fidelity and with similar cost, then there would be an issue. I don't think that's going to happen anytime soon, but I'm sure Illumina is looking at that long-term.