Hi all,
I am working with some polyploid organisms (ploidy not always known, but tetra and up) that we want to do some RADSeq / CRoPS sequencing with. These are organisms for which I have no reference genome. I am interested in clarifying the phylogeography of some species, but this is not my only aim.
I have been so far working with the Stacks software. Previously this was great as I was working with diploid (mammalian) organisms; however, now I have these polyploids and I read that Stacks is not built to work with polyploid organisms (although there are some suggestions as to how one can tweak the parameters a bit to try to get it working).
I have also read the paper by Peterson et al that details an alternative approach for dealing with RADSeq data, in this case specifically double-digest radseq. In this article, they seem to me to suggest that this approach would be better suited for polyploid organisms because it uses a "ploidy-aware" quality filter in place of the Stacks multinomial-based likelihood model which assumes a certain (diploid) allelic ratio.
My questions:
Thanks very much,
Mario
P.S. Forgive the cross-posting to Biostars. Not sure what the etiquette is on repeat questions but I'm sure there's a lot of overlap between the two sites.
I am working with some polyploid organisms (ploidy not always known, but tetra and up) that we want to do some RADSeq / CRoPS sequencing with. These are organisms for which I have no reference genome. I am interested in clarifying the phylogeography of some species, but this is not my only aim.
I have been so far working with the Stacks software. Previously this was great as I was working with diploid (mammalian) organisms; however, now I have these polyploids and I read that Stacks is not built to work with polyploid organisms (although there are some suggestions as to how one can tweak the parameters a bit to try to get it working).
I have also read the paper by Peterson et al that details an alternative approach for dealing with RADSeq data, in this case specifically double-digest radseq. In this article, they seem to me to suggest that this approach would be better suited for polyploid organisms because it uses a "ploidy-aware" quality filter in place of the Stacks multinomial-based likelihood model which assumes a certain (diploid) allelic ratio.
My questions:
- Does anyone has any experience working with this sort of data or either of these programs?
- Any recommendations regarding how to approach this kind of data with Stacks or with another program?
- Any further caveats or advice?
Thanks very much,
Mario
P.S. Forgive the cross-posting to Biostars. Not sure what the etiquette is on repeat questions but I'm sure there's a lot of overlap between the two sites.