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Old 01-11-2017, 06:47 AM   #1
LMM
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Default 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!
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Old 01-11-2017, 08:43 PM   #2
Brian Bushnell
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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?
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Old 01-12-2017, 08:19 AM   #3
gringer
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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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