aligning to reference genome or de novo?

[age87]

My organism doesn't have a reference genome, but a closely related species, the deer mouse (approx. 4 my diverged), has one but only assembled at the scaffold level.

Is it better to align to a good quality ref. genome but that is about 50 my diverged (Ratus norv) assembled at the chromosome level, or to fraft genome of the less diverged one?

There are intermediates also, like the chinese hamster.

Thanks!

[luc]

Could you tell us what you want to know about your amples/species?
My guess is you would be better of aligning to the deer mouse for most purposes.

[age87]

My species is the white-footed mouse (P.leucopus) and I want population genetic parameters and selection coefficients. I'm using stacks.