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Old 07-21-2015, 09:58 AM   #1
SNPsaurus
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Location: Eugene, OR

Join Date: May 2013
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Default nextRAD publication

We at SNPsaurus quite frequently get asked about publications using nextRAD. Of course, it take a while to go from genotyping data to publication! Today a paper using nextRAD was published at PeerJ:

Russello MA, Waterhouse MD, Etter PD, Johnson EA. (2015) From promise to practice: pairing non-invasive sampling with genomics in conservation. PeerJ 3:e1106 https://dx.doi.org/10.7717/peerj.1106

Paul and I appreciate Mike Russello including us on this publication, and I think it highlights some of the advantages of nextRAD genotyping, such as getting reliable sequence libraries made from just 60 hair follicles per sample.
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Old 02-17-2016, 09:06 AM   #2
etwatson
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Location: Los Angeles, CA

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Congratulations. The nextRAD method looks promising for our research. Our model organism for evolutionary research, Tigriopus californicus, is very small and DNA extraction yields have proven to be too little for traditional RAD-seq and ddRAD methods.

I am interested in genotyping F4 RIL (sib-sib) individuals from divergent population crosses. On the one hand, we shouldn't need too many markers for this study, but on the other, many sites may drop out in divergent regions of the genome (up to 6%).

I am wondering, since our individual extractions are highly variable and yield ~ 40 ng of DNA on average, how much do you expect us to lose based on variation in DNA yield? Normalizing input DNA at such a low concentration, and for many samples could get hairy...

Thanks!

- Eric
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Old 02-17-2016, 12:45 PM   #3
SNPsaurus
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Hi Eric, I'll e-mail you a follow up on this.
Eric
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