RAD seq degraded DNA

[cdbarratt]

Hi everyone,

I work with RAD seq [Sbf1] on large genomes (around 6Gb), and I am looking for a suggestion regarding the best strategy for degraded DNA in a standard (non-ddRAD) RAD protocol?

I want to call SNPs from a library of degraded DNA samples (high molecular weight but short fragments) and compare this with SNPs from a library of non-degraded samples that is already prepared. I know we will get fewer tags in the degraded samples but we want to get a subset of SNPs that are present in both libraries and suitable for phylogenies.

If anyone has any suggestions/experience with this I would be most grateful.

Cheers,
Chris

[SNPsaurus]

You might end repair the degraded DNA, blunt ligate Y-adapters, cut with SbfI and ligate SbfI overhang adapters. If you have degraded DNA it is hard to cut and then shear efficiently. Fortunately you can get a phylogeny without the highest quality data, because you probably aren't going to get that!

[cdbarratt]

Thanks for the reply SNPsaurus, I appreciate it!
I will look into this, phylogenies is our main goal so hopefully we can get some decent results.

Thanks!