Lorenzo Bertola

Hello Pasi! Thank you for the follow up. We are using the version from December 2023. Should we try a newer version? The names in the LOD output match the names and position of markers in the map file. We first ran orderMarkers for each LG 10 times and selected the order with the best likelihood, and then re-ran orderMarkers with the best order to produce the LOD file with the below command. java -cp lepmap/bin/ OrderMarkers2 \ data=2_filtered_LepMap_fam3 \ evaluateOrder=6_LepMap_fam3_${LG} \ improveOrder=0...

Hello Pasi! Thank you for the follow up. We are using the version from December 2023. Should we try a newer version? The names in the LOD output match the names and position of markers in the map file. We first ran orderMarkers for each LG 10 times and selected the order with the best likelihood, and then re-ran orderMarkers with the best order to produce the LOD file with the below command. java -cp lepmap/bin/ OrderMarkers2 \ data=2_filtered_LepMap_fam3 \ evaluateOrder=6_LepMap_fam3_${LG} \ improveOrder=0...

Hello Pasi, I am trying to do some testing using the LOD output matrix from the orderMarkers module, but I am struggling to understand what the positions in the columns represent. For a single linkage group I mapped 793 markers across 3 families. The resulting maps have: - female map: 101 unique positions - male map: 61 unique positions - sex-averaged map*: 157 unique positions. The LOD file has the correct number of rows (793), one row per mapped marker, but it only has 148 columns, thus 147 unique...

Hello Pasi, I am going back to some old results and am still confused over this topic. I will try and rephrase my question. When I run OrderMarkers with informativeMask=1 / informative Mask=13, I expect to obtain a map with only male positions, as no recombination events from the female parent are being used. BUT I obtain a map with both male and female position. How is the female position obtained when running with only male informative markers? Cheers, Lorenzo.

Hello Pasi, I have some confusion regarding the output of orderMarkers when running sex-specific maps. In the output, all loci have been placed on both the male and the female map. This should not be possible as, for instance, male informative only loci should be able to be placed only on the male map. Output: marker_number male_position female_position 7544 0.000 0.000 7543 0.000 0.719 2285 0.000 0.719 1550 0.000 1.439 2674 1.449 1.439 657 1.449 1.439 Expected output: marker_number male_position...

Hello Pasi, I am starting a new linkage mapping project, and this time i'm looking at parentcall2 in more detail, and I'm wondering why is it doing some changes, and whether they are needed or not. I have genotype data from double-digest rad-seq-like sequencing. I obtained fastq files and called genotypes with stacks denovo. I have large families (100-300 F1 offspring). I have already filtered to retained only informative markers). My input data looks something like this (2 markers, displaying only...

Hello Pasi, I am starting a new linkage mapping project, and this time i'm looking at parentcall2 in more detail, and I'm wondering why is it doing some changes, and whether they are needed or not. I have genotype data from double-digest rad-seq-like sequencing. I obtained fastq files and called genotypes with stacks denovo. I have large families (100-300 F1 offspring). I have already filtered to retained only informative markers). My input data looks something like this (2 markers, displaying only...

Hello Matthieu, I used to have a similar issue, and I solved it by running separate chromosomes on the two parents individually (using informative mask). This returned the expected number of LG for each parents. I then match the grouping between the two, and sometimes filter markers that are assigned to different LGs, and then use that LG assignment to run OrderMarkers. I'm not sure if that's your issue, but maybe it can help.