Dear Pasi,
Thank you for your Lep-Map3.
When I do some tests for chr1 with one family (parents and 80 offspring individuals), I got 24176 snps after SeparateChromosomes2 Module on LG1, and then I put them into OrderMarker2 Module.
My questions is:
Does the OrderMarker2 Module have same function as 'maxDistance=NUM' of OrderMarker Module in LepMAP2, maxDistance can set the maximum recombination ratio.
As question 1, does the OrderMarker2 Module have same function as ''removeDuplicates" of OrderMarker Module in LepMAP2? In order4.txt, too many markers located at the same place in genetic map, the 'removeDuplicates' can solve the problem? How to solve the problem in LM3?
To build the map with only useful makers, I use "identicalLimit = 0.01 and maskIgnoreParentOrder = 1" to reduce makers, but markers are still 24176. What caused this result?
The result file of OrderMarker2 Module has the genetic positons of parents, but how to build the offsprings' genetic map or get the genecit positons of offspring?
For the parents map, I found that The parental genetic distance varies greatly (133cM vs 82cM). This is not correct , is it? What do you think caused this and how to solve it?
I am sorry for asking so many questions and looking forward to your reply. Thank you so much!!!!
Many thanks,
Felix
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Thank you for your question. Indeed, the philosophy of map construction is quite different in LM3 than in LM2 and in some other software.
There is no maxDistance nor removeDuplicates in LM3. You can figure out markers with same map position after LM3 run but there is typically no (good) reason to remove such markers. I don't see many markers as a problem.
The parameters, IdenticalLimit and maskIgnoreParentOrder, you are changing do not change the behaviour.
Linkage map is always constructed for the parents. Map does not extend to offspring without offspring crosses (e.g. F2, F3, ...).
On many species, that parental maps differ in length (heterochiasmy).
Cheers,
Pasi
Last edit: Pasi Rastas 2021-05-07
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Dear Pasi,
Thank you for your Lep-Map3.
When I do some tests for chr1 with one family (parents and 80 offspring individuals), I got 24176 snps after SeparateChromosomes2 Module on LG1, and then I put them into OrderMarker2 Module.
My questions is:
For the parents map, I found that The parental genetic distance varies greatly (133cM vs 82cM). This is not correct , is it? What do you think caused this and how to solve it?
I am sorry for asking so many questions and looking forward to your reply. Thank you so much!!!!
Many thanks,
Felix
Dear Felix,
Thank you for your question. Indeed, the philosophy of map construction is quite different in LM3 than in LM2 and in some other software.
There is no maxDistance nor removeDuplicates in LM3. You can figure out markers with same map position after LM3 run but there is typically no (good) reason to remove such markers. I don't see many markers as a problem.
The parameters, IdenticalLimit and maskIgnoreParentOrder, you are changing do not change the behaviour.
Linkage map is always constructed for the parents. Map does not extend to offspring without offspring crosses (e.g. F2, F3, ...).
On many species, that parental maps differ in length (heterochiasmy).
Cheers,
Pasi
Last edit: Pasi Rastas 2021-05-07