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Old 06-29-2017, 10:17 PM   #7
SNPsaurus
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Location: Eugene, OR

Join Date: May 2013
Posts: 521
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I enjoy all the RAD variants and they are interesting how they solve different problems. In their case, they were sequencing on a MiSeq with a 600 cycle run, so the cost per read is going to be extremely high. The repetitive element in their genome made it important to try out different restriction enzyme combinations, and they didn't want to order a bunch of adapters for each try. So these selective pressures led to evolution of the method and a local optima for their situation!

Sometimes for publication, authors compare their method to others in order to demonstrate why it should be published, and it is difficult to do that impartially. They need to show it is not a local optima but generally optimal to get the most interest. But this is difficult, since others will say, "why work hard to multiplex on a MiSeq, costing $1800 for 25MM reads, when it is cheaper to just run it on a HiSeq4000, costing $1100 for 400MM reads?"
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