Lidia de los Ríos Pérez

Hi Pasi, Thank you very much for your answer. Just to make sure I understood correctly... So far, I did 10 replicates of OrderMarkers2 for each LG. In order to not have to repeat this step including "hyperPhaser=1" and/or "phasingIterations=3", I could: First, choose the replicate with the highest likelihood for each LG. Then, rerun OrderMarkers2 for the chosen replicate with java -cp bin/ OrderMarkers2 evaluateOrder=OM_R${i}_LG${j}.txt data=data_F.call improveOrder=0 randomPhase=1 numThreads=16...

Hi Pasi, Thank you very much for your answer. Just to make sure I understood correctly... So far, I did 10 replicates of OrderMarkers2 for each LG. In order to not have to repeat this step including "hyperPhaser=1" and/or "phasingIterations=3", I could: First, choose the replicate with the highest likelihood for each LG. Then, rerun OrderMarkers2 for the chosen replicate with "improveOrder=0 evaluateOrder=file randomPhase=1" Is this correct? Or should I rerun the OrderMarkers2 for all the replicates...

Hi Pasi, Sorry to bother you again. Do you by chance have any suggestion concerning my previous message? I would like to make sure I do things the best possible way. Thanks in advance! Cheers, Lidia

Hi Pasi, First of all thank you very much for all your help. I have done as suggested and it looks alright. However, for the OrderMarkers2 step, I am getting the following warning for most of the chromosomes: Warning: Inconsistencies in phasing, please try using randomPhase=1 and/or hyperPhaser=1 in OrderMarkers2 Enabling hyperPhaser... My command line is: java -cp bin/ OrderMarkers2 map=JS_map50_LL30_LD10.txt data=data_F.call chromosome=1 numThreads=16> OM_R1_LG1.txt 2> OM_R1_recombinations_LG1.txt...

Hi Pasi, First of all thank you very much for all your help. I have done as suggested and it looks alright. However, for the OrderMarkers2 step, I am getting the following warning for most of the chromosomes: Warning: Inconsistencies in phasing, please try using randomPhase=1 and/or hyperPhaser=1 in OrderMarkers2 Enabling hyperPhaser... My command line is: java -cp bin/ OrderMarkers2 map=JS_map50_LL30_LD10.txt data=data_F.call chromosome=1 numThreads=16> OM_R1_LG1.txt 2> OM_R1_recombinations_LG1.txt...

Dear Pasi, I hope you are doing great. I am wiriting to you because I would like to know if Lep-Map3 somehow checks for errors in the patterns of inheritance, either in the ParentCall2 or in Filtering2 module. Thanks in advance! Cheers, Lidia

Dear Pasi, Just to make sure I understood correctly. From the file obtained in SC2 (SC_map50.txt) I should change all the groups 25..N to 0, so that they are counted as singles and they are taken into consideration in the JoinSingles2All step. Is this correct? Thanks! Cheers, Lidia

Dear Pasi, Thank you very much for your quick answer and suggestions. I have done the JoinSingles2All step as you suggested, one with lodDifference=5 and one with lodDifference=10. java -cp bin/ JoinSingles2All map=SC_map50.txt data=data_F.call lodLimit=30 lodDifference=5 iterate=1 numThreads=16> JS_map50_LL30_LD5.txt java -cp bin/ JoinSingles2All map=SC_map50.txt data=data_F.call lodLimit=30 lodDifference=10 iterate=1 numThreads=16> JS_map50_LL30_LD10.txt Questions: Is it correct to enable the iteration...