Lorenzo

Hello Pasi, I have an additional question. When I run FitStepFunction, the output has a number of rows that is correlated to the number of markers per linkage group for i in {1..21}; do cat run17_T6_pval001_female_LG${i} | wc -l; done 3198 2876 1805 2116 1871 1937 1857 1728 1523 1728 1467 1521 1485 1482 1224 1344 1284 1214 1036 1037 1122 But then the outputs of EstimateRecombination all have the same number of rows. I am struggling to understand why that might be? for i in *recombination; do cat...

Hello Pasi, Replying here for completeness and for future users. I have now encountered this pattern twice. Once with the multifamily design described above, and once with single families of 2 parents x ~100 F1 offspring. For the multifamily map we were able to fix this by using the hyperPhaser parameter and increasing the number of iterations the OrderMarkers module was run for. For the single family maps we tried everything in OrderMarkers, but nothing fixed it, so we are now using FitSteFunction...

Hello Pasi, Thank you very much for your reply. I will attempt to expand on your three suggested options, to ensure that we understand them correctly, and for future reference for other users: Three ways to fix this: 1) evaluate the map in the physical order (evaluateOrder=phys_order.txt, improveOrder=0) The rationale for this option is to constrain the order (1st, 2nd, 3rd, etc) of markers to their physical position on the assembly during the OrderMarkers2 step, to ensure a monotonically increasing...

I think I might have answered this question to myself. The rows with four columns ending with male|female|average marey are the adjusted marey map, with physical position (column 1), map position (column 2), the 'sex' (i.e., male|female|average, column 3), and the marey map identifier (marey, column 4). I just need some clarification as to the 'density' rows. What is the value in the density column (column 2), is that the recombination rate? Once again, thanks for this software :) Cheers, Lorenz...

Dear Pasi, Thanks once again for very useful software and tools. We have been trying to use the FitStepFunction and EstimateRecombination modules to estimate local recombination rate using linkage maps produced with LepMap3. I have been able to run FitStepFunction and EstimateRecombination as you suggest in the LepMap and LepAnchor wiki. But I am not at a loss for how I should interpret the EstimateRecombination output. What is included in the output, and how can I use that to integrate the recombination...

Hello Pasi, We are building linkage maps with LepMap3 using 9 families (from 7 males and 3 females). Data is highly accurate (SNP Chip) and we have1,962 offspring in total (smallest family has 99 offspring). When we build maps from single families they look really good (1:1 match between male and female map, no off diagonal markers). But when we join multiple families, we start seeing 'parallel lines' (see attached image for an example on one chromosome). Notably, the map with this issue has the...