Hello All,
I'm working on a graduation project at University and as part of my investigation I must test the some genetic mapping tools (MapDisto, MSTMap and OneMap). However, I've had some problems with the simulated data for testing, and I want to know if you can give me some tips in how I could do this simulation.
Basically my algorithm does the following:
* Random positions -> simulating the positions along the chromosome
* Parent1 (Gametes) -> Fill it with random alleles that can take the values 0 or 1, that means (0,0) and (1,1) are homozygous, and (0,1) or (1,0) are heterozygous.
* Parent2 (Gametes) -> Fill it taking Parent1 as a base. In order to have different alleles in the same chromosome position from both parents.
* Population -> Take a gamete from parent1 and other from parent2, then I calculate the recombination frequency, using the Haldane function. This process generates a F1 population.
* Finally, I generate a F2 population from the previous one, following the same process.
Do I missing something in the process? Is the algorithm logic well proposed to do the simulation?
PD: The data must be generic, I only need to represent a F2-diploid-population, and maybe a polyploid population.
If you can help me on this I will be very gratefull.
Best Regards.
I'm working on a graduation project at University and as part of my investigation I must test the some genetic mapping tools (MapDisto, MSTMap and OneMap). However, I've had some problems with the simulated data for testing, and I want to know if you can give me some tips in how I could do this simulation.
Basically my algorithm does the following:
* Random positions -> simulating the positions along the chromosome
* Parent1 (Gametes) -> Fill it with random alleles that can take the values 0 or 1, that means (0,0) and (1,1) are homozygous, and (0,1) or (1,0) are heterozygous.
* Parent2 (Gametes) -> Fill it taking Parent1 as a base. In order to have different alleles in the same chromosome position from both parents.
* Population -> Take a gamete from parent1 and other from parent2, then I calculate the recombination frequency, using the Haldane function. This process generates a F1 population.
* Finally, I generate a F2 population from the previous one, following the same process.
Do I missing something in the process? Is the algorithm logic well proposed to do the simulation?
PD: The data must be generic, I only need to represent a F2-diploid-population, and maybe a polyploid population.
If you can help me on this I will be very gratefull.
Best Regards.
