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Thread | Thread Starter | Forum | Replies | Last Post |
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RNAseq sample files | ocs | Bioinformatics | 5 | 07-29-2011 03:40 PM |
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#1 |
Junior Member
Location: Athens, Ohio Join Date: Jan 2017
Posts: 8
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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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#2 |
Super Moderator
Location: Walnut Creek, CA Join Date: Jan 2014
Posts: 2,707
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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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#3 |
David Eccles (gringer)
Location: Wellington, New Zealand Join Date: May 2011
Posts: 815
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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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