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  • #16
    In GBS methods (single or double digest) one can recognise the presence of repeat region or organelle fragments’ amplicons in prepped library and not to proceed to sequencing. I believe this is one aspect that they look at the establishment phase for new species. Users often utilise only 50% of their GBS reads because of low coverage and low number of common loci among samples but they still are happy getting around 1K polymorphic loci from their data. Some users repeat their samples in their submission to increase coverage. Obviously, number of useful fragments depends on study aim, population type, existence of reference genome and other factors. ddRAD as it has been described leaves sampling repeat region to chance.

    RAD-Seq is most comprehensive and probably more consistent version of the methods, but library prep costs can be prohibitive and can exceed sequencing costs.
    Last edited by nucacidhunter; 05-24-2014, 04:29 PM.

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    • #17
      Originally posted by maxbangs View Post
      Thank you for your comments nucacidhunter and SNPsaurus.
      I guess I should explain my math. I was trying to calculated the number of expected loci for a given size selection (300+/-36) so I calculated the proportion of DNA in the size selection (.47ng/19.4ng) and then multiple by the size of the genome (2.42Gbps) to get the number of bps with in the selection.
      Hi!

      Please, I would like to know if these concentration values of ng/ul are from real data, because I am doing ddRAD and I found similar concentration. But I didn't do qPCR yet to see if the final concentration is good for sequencing.

      Cheers

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