ddRADseq copy number variation

Question

[jingjin2203]

Hi All,

I was wondering if I can detect copy number variation using ddRAD seq? If so, could recommend some tools to achieve that? And how can I normalize the the data since in a pooled library each sample has 'slightly' different numbers of total reads?

Any comments and suggestions are welcomed!

Thank you!

[h.mon]

I can't "recommend" as I never used, but as it seems you don't know any software, so one is already an improvement:

YMAP: a pipeline for visualization of copy number variation and loss of heterozygosity in eukaryotic pathogens

Caveat: it is designed for small genomes.