LIYY

Dear Pasi, Have you finished the work that construct maps without any parents or grandparents? Thanks, LIYY.

Dear Pasi, How to set the threshold of L to define the QTL ? Thanks, LIYY

Hello Lorenzo, Thanks for your advice. I don't have any other offspring and don't know which one is the mother .I think that I have a common father and the father's 57 offspring,maybe I can only study the father's recombination.If It's ok,whatI need to do ? 1 offspring per family doesn't work.Could I make a pedgree file which hava one family with a father ,a virtual mother and 57 offspring ,and then abstact male map ? Thank you, LIYY

Dear Pasi, Thanks for your response. You are right,There are one individual per family.If it's not feasible for linkage mapping,could I make a virtual mother as a common mother of 57 families ?Then I abstact male map as final map . Could I do this ? Thank you, LIYY

Dear Pasi, There are only one common father and 57 individuals of 57 families in vcf,no mother and no grandparents.The format of two files is right.It works but no result .Can Lep-MAP3 not caculate this ? OR are there any threshold of miss ratio in one SNP ?I filted 0.2 ,but it's still no result . java -cp /lepmap3/lepmap3/bin ParentCall2 data=pedgree.txt vcfFile=CM008008.1.recode.vcf removeNonInformative=1 >CM008008.1.recode.parent.call Thank you, LIYY

Dear Pasi, Thanks for your response. I don't know how to set the ZLimit.In the wiki ,there isn't detail account of ZLimit.Are there only Z or/and W in the vcf when I run ParentCall2?the ZLimit number how to set?Does it depend on SNP number?or family number?The ParentCall2 how to distinguish Z or W ?My sex chromosome is named NC006127,should I change it to W in vcf?Z and W will be one linkage group or two ? Thanks, LIYY

Dear Pasi, How to do for W/Z chromosome ? Is it same as the autosomes?If not,how to do ?The file of SeparateChromosomes2 is filled Z ,but reported error. By the way,I saw that Number of called Z/X markers = 0 in the log .What is the meaning ?Sex chromsome ? Thanks, LIYY

Dear Pasi, How to do for W/Z chromosome ? Is it same as the autosomes?If not,how to do ? By the way,I saw that Number of called Z/X markers = 0 in the log .What is the meaning ?Sex chromsome ? Thanks, LIYY