Yess Alvarez

Dear Pasi, Thank you for clarifying my doubts! I have run OrderMarkers2 with improveOrder=1 to observe potential structural variations in CHR16. However, when I run the Marey map, the positions of the markers are dispersed. I'm confused about what this means. I share the command and the charts. > java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= ./order_CHR_phys/order_CHR16.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=1 > eval_order/eval_CHR16_run1.2.txt...

Dear Pasi, Thank you for clarifying my doubts! I have run OrderMarkers2 with improveOrder=1 to observe potential structural variations in CHR16. However, when I run the Marey map, the positions of the markers are dispersed. I'm confused about what this means. I share the command and the charts. > java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= ./order_CHR_phys/order_CHR16.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=1 > eval_order/eval_CHR16_run1.2.txt...

Dear Pasi, Thank you for clarifying my doubts! I have run OrderMarkers2 with improveOrder=1 to observe potential structural variations in CHR16. However, when I run the Marey map, the positions of the markers are dispersed. I'm confused about what this means. I share the command and the charts. > java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= ./order_CHR_phys/order_CHR16.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=1 > eval_order/eval_CHR16_run1.2.txt...

Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...

Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...

Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...

Dear Pasi, I've managed to obtain 24 LGs as expected according to the reference genome (24 chromosomes). This is the command I used: java -cp bin/ OrderMarkers2 useKosambi=1 numThreads=18 evaluateOrder= order_CH1.phys data=pejerrey.call sexAveraged=0 minError=0.005 phasingIterations=3 improveOrder=0 calculateIntervals=intervals_markers_CH1.txt > eval_CHR1.txt But I have some questions regarding the results: I have created LMPlots for each one to observe the order of the markers, and I noticed that...

Dear Pasi, Thanks a lot for your help! I followed your advice and managed to get the files. However, while analyzing numeric_snps.txt, I found that my LG1 doesn't correspond to chromosome 1. In fact, it contains markers for chromosome 5 (165 markers) and chromosome 18 (151 markers). I think, I could try running SeparateChromosome2 for this LG and observe if they separate. Is this possible? If so, how should I proceed? On the other hand, I found two linkage groups (LG21= 60 markers and LG24=53 markers)...