How to choose the right parameters in chrompainter for badMIXTURE

[salonso65]

Dear Dan

I am trying to use badMIXTURE but I have the following doubts:

1.- If I have already results from chomopainter in which I have used the -a option (all inds x all inds), and I want to use that for badMIXTURE, should I:

a) just sum chunks for all inds within the same pop, and generate a inds x pops matrix?
or
b) run again chromopainter this time using the -f option (inds x pops)?

2.- In addition, should I use the option in which all pops are D (donors) and R (recipients) ? or...

3.- should I select some pops as D and some as R (or D+R)? For this case, as a guide, imagine an ADMIXTURE plot with 3 pops in which popA is all red, popB is all green and popC is 50%green, 50%red. Should I select pops A and B as "only donors"? and C as "D and/or R"? Or shoud I use all pops as "D and R"?

I am asking because I think perhaps this could have an influence in the marginals, and consequently, in the inferences made from the badMIXTURE plots.

Thanks in advance

[leyanKk]

Hello, has your issue been resolved? I have another question: which output file from chomopainter should I use as the input N x P matrix for badmixture?