SEQanswers - View Single Post - ERCC spike-ins for prokaryotes

Bukowski · 02-27-2019, 06:33 AM

I don't think they say it's only good for eukaryotes, just that it mimics the nature of eukaryotic transcripts in terms of nucleotide content, size distribution, polyadenylation etc. I think the bigger concern using them for prokaryotes is probably that a chunk of the ERCC spike ins are derived from bacterial sequences in the first place.

If you're concerned about the derivation of the ERCC sequences, then there are artificial spike-in's available: https://www.rna-seqblog.com/spliced-...g-experiments/ (I would link to the sequins site, but there appears to be a configuration issue on their webserver)

Given that you "already see many people use ERCC spike-ins with prokaryotes" what kind of additional validity are you looking for?

02-27-2019, 06:33 AM	#2
Bukowski Senior Member Location: UK Join Date: Jan 2010 Posts: 390	I don't think they say it's only good for eukaryotes, just that it mimics the nature of eukaryotic transcripts in terms of nucleotide content, size distribution, polyadenylation etc. I think the bigger concern using them for prokaryotes is probably that a chunk of the ERCC spike ins are derived from bacterial sequences in the first place. If you're concerned about the derivation of the ERCC sequences, then there are artificial spike-in's available: https://www.rna-seqblog.com/spliced-...g-experiments/ (I would link to the sequins site, but there appears to be a configuration issue on their webserver) Given that you "already see many people use ERCC spike-ins with prokaryotes" what kind of additional validity are you looking for?