I haven’t seen the specification but a lot of rna-SEQ is cheap high volume tag counting, rightly or wrongly, and therefore very short read bound. Nanopore tends to be used more for full length cDNA or direct RNA with modifications which are not as easy or even possible on ILMN, yes they cost more.
On the cost question, its not ILMN vs nanopore, its Plasmidsaurus vs academic core. It’s normally difficult for a private company to compete with cores because they have to fully cost things including the instrument capital. Academic cores can often write off the capital and only refer costs relative to consumables. So how P is competing with that is a mystery, unless ILMN are now offering pricing more like ONT which is effectively consumable only.
I think it highlights an existing user base for ILMN that only want lots of short read tags and probably dont care about machine ownership or even TAT so its handle cranking. AFAIK Nanopore haven’t targeted high volume short tag counting applications, probably because its already dominated by ILMN and also because their long read platform isn’t tuned up for it.
I haven’t seen the specification but a lot of rna-SEQ is cheap high volume tag counting, rightly or wrongly, and therefore very short read bound. Nanopore tends to be used more for full length cDNA or direct RNA with modifications which are not as easy or even possible on ILMN, yes they cost more.
Yes, the fact that they appear to have selected Illumina here highlights the cost issue.
On the cost question, its not ILMN vs nanopore, its Plasmidsaurus vs academic core. It’s normally difficult for a private company to compete with cores because they have to fully cost things including the instrument capital. Academic cores can often write off the capital and only refer costs relative to consumables. So how P is competing with that is a mystery, unless ILMN are now offering pricing more like ONT which is effectively consumable only.
I think it highlights an existing user base for ILMN that only want lots of short read tags and probably dont care about machine ownership or even TAT so its handle cranking. AFAIK Nanopore haven’t targeted high volume short tag counting applications, probably because its already dominated by ILMN and also because their long read platform isn’t tuned up for it.
On a slightly tangential note, what read lengths are used for RNA-Seq?