I'm going to start with NGS methodologies from environmental samples and some people have told me they obtain prokaryotic and eukaryotic cDNA simultaneously by hexamer primed reverse transcription, but in the sequencing company they want me to separate eukaryotic from prokaryotic cDNA, having of course two samples instead of one.

Can anyone tell me if that is the best strategy or if they just want to charge me more?

Thank so much

Regards

Kathia L