Hi Everyone,
We're trying to do some RAD sequencing on frogs that have large genomes (9-10gb). We've tried some samples with single digest RAD using ApeKI (another lab was prepping some samples with ApeKI and threw some of our frogs in). We found almost no SNPs between samples, I believe because we had too many fragments and really low coverage. So we're now considering ddRAD with a rare-cutting enzyme.
Does anyone have any suggestions of restriction enzymes to use for amphibians with large genomes? Does anyone have advice for RAD with large-genome amphibians? The species is Rana boylii (and a few other closely related species), and we plan on doing size selection using either gel excision or SPRI beads. We want to put about 120 individuals on a HiSeq lane, so we could handle a relatively large number of fragments.
Thanks very much!
We're trying to do some RAD sequencing on frogs that have large genomes (9-10gb). We've tried some samples with single digest RAD using ApeKI (another lab was prepping some samples with ApeKI and threw some of our frogs in). We found almost no SNPs between samples, I believe because we had too many fragments and really low coverage. So we're now considering ddRAD with a rare-cutting enzyme.
Does anyone have any suggestions of restriction enzymes to use for amphibians with large genomes? Does anyone have advice for RAD with large-genome amphibians? The species is Rana boylii (and a few other closely related species), and we plan on doing size selection using either gel excision or SPRI beads. We want to put about 120 individuals on a HiSeq lane, so we could handle a relatively large number of fragments.
Thanks very much!
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