Xochitl Granados

I really appreciate your answer, I think the easiest way to analyze the data is with two dummy parents, thank you Best regards

Hi Pasi, I have data from GBS for an haploid (conifer) population and also the information of the mother (diploid) and I want to analyze them together to make a linkage map, but I would like to know what would be the best way to encode it, as an F2 with information only from the maternal inheritance? and for male no information? Or to eliminate the information for the diploid mother and to make linkage map only with the haploid data? Thank you Best regards

Thank you, I will carefully review the output files. Thanks for the suggestions for the part of mapping to the reference, the data from PacBio will be from the same individuals, I hope this will help in this part. Thank you very much for your comments and suggestions

Dear Pasi I have doubts about how to evaluate the quality of the maps I got from LepMap3, my data comes from haploid tissue and strictly from maternal inheritance, I have 183 individuals from two populations, but my snps are de novo, we do not have a reference genome, and I would like to use this map to scaffold our reads from PacBio. My main doubt is that the markers are not in order with their physical position, so when trying to graph the points are scattered. Previously you had answered me how...

Dear Pasi I have some doubts about the OrderMarkers2 output files and the .call file, my data comes from haploid tissue and strictly from maternal inheritance 1) I tried plotting the marker number with the physical position but my data is totally scattered, I checked the graphviz DOT charts and it seems that the maps are ok (attached the images), there are no red lines. The parameters I used are: OrderMarkers2 map=map23_js.txt data=p_fil.call chromosome=1 numThreads=16 selfingPhase=1 2) In the filtered...

Dear Pasi, I expect 12 linkage groups, I found that lodLimit=24 is perfect it gave 12 groups Thanks for your valuable comments, Xochitl

Dear Pasi, Thanks for your valuable comments I have a doubt about the lodLimit and the distribution of the markers, since I got a nonuniform distribution I increase the lodLimit as mentioned in other comments but I don’t know if it was too high. I tried from 18 to 40 and the best distribution so far is 40 but I do not know if something is wrong, could you give me some advice?, thank you. I used the following options -SeparateChromosomes2 data=dataAll_fil.call lodLimit=18 distortionLod=1 numThreads=...

Dear Pasi, Thank you very much for your reply, I send you a screenshot of the snps.vcf file. I think it is already in a diploid format. I tried to run the ParentCall2 function using the pedigree file you sent and got 170545 markers but with some warnings, I also attach an image of ParentCall2 results. Thanks, Xochitl