Sample size for RNASeq

LMM · 01-11-2017, 06:47 AM

We are a lab new to sequencing and are preparing for an RNAseq on a soil transcriptome (multiple members, specifically targeting a couple gene families). Given cost constraints, we would like to be as efficient as possible with our flowcells/ chips. Is there an ideal number of samples we should include in our study?
Thanks!

Brian Bushnell · 01-11-2017, 08:43 PM

Not sure if I'll be able to answer this question, but certainly, I think it would help if you could clarify. What are your goals? And what do you mean by "targeting" - are you doing some kind of enrichment or selective amplification, or is it whole-transcriptome? Also, what kind of metagenomic complexity do you expect (or what kind of soil is it)? What kind of platform are you using?

gringer · 01-12-2017, 08:19 AM

Do a pilot study of a single sample, and look at rarefaction curves to work out approximately how many reads are needed to cover the metagenomic complexity.

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01-11-2017, 06:47 AM	#1
LMM Junior Member Location: Athens, Ohio Join Date: Jan 2017 Posts: 8	Sample size for RNASeq We are a lab new to sequencing and are preparing for an RNAseq on a soil transcriptome (multiple members, specifically targeting a couple gene families). Given cost constraints, we would like to be as efficient as possible with our flowcells/ chips. Is there an ideal number of samples we should include in our study? Thanks!

01-11-2017, 08:43 PM	#2
Brian Bushnell Super Moderator Location: Walnut Creek, CA Join Date: Jan 2014 Posts: 2,707	Not sure if I'll be able to answer this question, but certainly, I think it would help if you could clarify. What are your goals? And what do you mean by "targeting" - are you doing some kind of enrichment or selective amplification, or is it whole-transcriptome? Also, what kind of metagenomic complexity do you expect (or what kind of soil is it)? What kind of platform are you using?

01-12-2017, 08:19 AM	#3
gringer David Eccles (gringer) Location: Wellington, New Zealand Join Date: May 2011 Posts: 815	Do a pilot study of a single sample, and look at rarefaction curves to work out approximately how many reads are needed to cover the metagenomic complexity.