Xuemei Tang

Hi Pasi, Thanks for your quick response! simpleConvert.awk works perfectly. I would like to check “00” means missing data? When sexAveraged=0, LM3 use all markers to generate male/female position? e.g. for male position, use only male informative or male only + both? I know users do not need to set these parameters, but I would like to understand how Lep-MAP3 works theoretically. Best, Xuemei

Hi Pasi, I tried running SeparateChromosomes2 with the reference genome chromosome information, but it didn’t work (it shows 12 linkage groups instead of 9). Please let me know what I did wrong. Thanks for your help! Xuemei java -cp /programs/Lep-MAP3/bin SeparateChromosomes2 data=p_fil.call usePhysical=1 0.01 map=physical.txt > map_physical.txt 2>error_phy.txt awk '(NR>=7)' p_fil.call | cut -f 1,2 >snps.txt paste snps.txt map_physical.txt | cut -f 1-3 > map_physical_lgs.txt error_phy.txt Loading...

Hi Pasi, Thanks a lot for your answer! I have two more questions: 1. Is there any way to export genotype data without imputation and correction? 2. For the female and male genetic maps, LM3 only uses the markers that are informative in the female/male parent, or use markers informative in female/male parent and both parents? eg, for female map, only use female informative markers or use female informative and both parents informative markers? Best, Xuemei

Hi Pasi, Thanks a lot for your answer! I have two more questions: 1. Is there any way to export genotype data without imputation and correction? 2. For the female and male genetic maps, it only uses the markers that are informative in the female/male parent, or use markers informative in female/male parent and both parents? eg, for female map, only use female informative markers or use female informative and both parents informative markers? Best, Xuemei

Hi Pasi, Sorry to bother you again! I would like to know how to set and use the parameter usePhysical. I tried usePhysical=1 0.0001, but it didn’t change the SeparateChromosomes2 results. How exactly does usePhysical work in SeparateChromosomes2 and OrderMarkers2? usePhysical=1 NUM Use physical positions in the marker separation, [not set, NUM=0.01] penalise markers in different contigs by log10(NUM) usePhysical=NUM1 NUM2 (NUM1>1) Use physical positions in the marker separation, penalise markers...

Hi Pasi, Thanks a lot for your answer! I set lg=0 and was able to get 9 LGs by using reference genome chromosome information (physical.txt). Best, Xuemei java -cp /programs/Lep-MAP3/bin SeparateChromosomes2 data=p_fil.call map=physical.txt lg=0 > map_physical.txt Loading file No grandparents present in family FLBG_0502_FLBG_0503 Number of individuals = 150 Number of families = 1 File loaded with 705 SNPs Number of individuals = 150 excluding grandparents Number of families = 1 computing pairwise...

Hi Pasi, Thanks for your quick response! I thought SeparateChromosomes2 will use reference genome chromosome information (physical.txt) to decide the number of LGs. Xuemei

Hi Pasi, I tried running SeparateChromosomes2 with the reference genome chromosome information, but it didn’t work (it shows 12 linkage groups instead of 9). Please let me know what I did wrong. Thanks for your help! Xuemei java -cp /programs/Lep-MAP3/bin SeparateChromosomes2 data=p_fil.call usePhysical=1 0.01 map=physical.txt > map_physical.txt 2>error_phy.txt awk '(NR>=7)' p_fil.call | cut -f 1,2 >snps.txt paste snps.txt map_physical.txt | cut -f 1-3 > map_physical_lgs.txt physical.txt 1 161046...