Erin Campbell

Hi again Pasi, Can you provide some information about what the file format containing the physical marker order should look like in order to use the evaluateOrder=file.txt option? Thanks, Erin

Ok thanks Pasi, this was very helpful! Erin On Mon, May 27, 2019 at 12:44 AM Pasi Rastas lep-map@users.sourceforge.net wrote: Dear Erin, Even one family data has such discrepancies (markers informative on male, female or both). And you probably have too few markers with single families. If you want discrepancy free map, just evaluate the map in the physical order. Create marker order used in your Mareys and use (evaluateOrder=file and improveOrder=0, you can also use hyperPhaser and adjust scale...

Hi Pasi, Thanks so much for your response. So, I think what you're saying is that the discrepancies between linkage map position and scaffold position are due to the inclusion of multiple families, and that marker ordering might be improved by running LepMap on individual families instead of all 13? If so, thank you for that insight, and I will check to see if this improves the marker ordering. Regarding the informativeMask parameter, I used 23 because I got more markers overall and fewer ambiguous/uninformative...

Hi Pasi, I've been using LepMap3 to build a linkage map using crossing data from 13 families of beetles (parents and full-sib F1, F2 crosses) with 226 individuals and about 10,000 markers. I plan on using the linkage map to assess the quality of the reference genome assembly for my organism, which already has chromosome-sized scaffolds, as well as to look for inversions in the crossed individuals. I have been able to get the expected number of chromosomes in my map (12), and each of those linkage...