ferracimo/3p-clr

3p-clr's Issues

How to calc "num" column in CalcDriftsF3/test_input.txt

Hi @FerRacimo,
How do I calculate the "num" column to use the DriftsF3 scripts?
thanks,
@stsmall

Too many steps in routine qromb: Numerical result out of range

Hi @FerRacimo,
I seem to be running into the above error. Once I get the error, the program continues running and only produces the error output line over and over again. I can provide an input file if it would help.
Here is my command line: 3P-CLR/src/threepclr "${file}" "${file}.output" 20 100 0.0025 0.01353,0.0025,0.4460 NA
thanks,
@stsmall

What does the weight file mean?

Dear Fernando,

I am trying to run 3P-CLR on our fish population resequencing data.

Given three populations: Outgroup, A and B, which LDHat recombination map should I use? I noticed that the note recommended using only the outgroup rec map, I'm wondering what the reason is behind this.

I couldn't seem to find more details about the LD weight file. What is its format and which population should I be using for this weight file?

What happens if the recombination maps differ a lot between the outgroup and A/B?

Thank you!

Best Regards,
Ray

how to deal with input in own data

Dear Fernando,
I'm sorry to bother you, I'm an outdoor for bioinformatics, so always have many problems of 3P-CLR that seem like a superb tool to fit my subject. I am trying to run 3P-CLR on our duck population genomics data, but I've just got data like vcf, map, fam and so on. I have no idea that you mentioned about Derived alleles and Sampled alleles in computing Drift rate of ABC populations. Usually, we were known that Derived alleles and Ancestral alleles, so I'm so confused about this question. Finally, I don't know how to deal with my data to fit 3P-CLR or just our data is not enough to use it. We can use our data to run CLR and XP-CLR, so I think that maybe it's my fault that don't know how to organize our data to fit 3P-CLR.

Thank you!

Best Wish,
Rui