Activity for Lidia de los Ríos Pérez
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Lidia de los Ríos Pérez modified a comment on discussion General Discussion
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...
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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...
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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
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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...
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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...
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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
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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
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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...
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Dear Pasi, Thank you very much for your quick answer. I have a few more questions. For the next step (JoinSingles2All) how can I choose the LodLimit to use? Should it start with a LodLimit larger than the one I used for SeparateChoromosomes2? For example, if I use the results from SeparateChromosomes2 with lodLim=50, should I use for JoinSingles2All a lodLimit=51 ? Thanks in advance! Cheers, Lidia
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Hi Pasi, I am new at working with linkage maps and therefore I would like to know if what I have done so far makes sense. I am working with 6 families; two of them have the same father and the number of progeny for each of them is very different. Looks like this Fam Male Female Progeny N2 SL387 SL389 29 N3 SL390 SL392 98 N4 SL393 SL394 3 N5 SL395 SL397 224 N6 SL400 SL399 15 N7 SL400 SL402 6 I have a total of 1,356,797 SNPs obtained by following the GATK pipeline. The 1,356,797 SNPs are all bi-allelic...
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Hi Pasi, I am new at working with linkage maps and therefore I would like to know if what I have done so far makes sense. I am working with 6 families; two of them have the same father and the number of progeny for each of them is very different. Looks like this Fam Male Female Progeny N2 SL387 SL389 29 N3 SL390 SL392 98 N4 SL393 SL394 3 N5 SL395 SL397 224 N6 SL400 SL399 15 N7 SL400 SL402 6 I have a total of 1,356,797 SNPs obtained by following the GATK pipeline. The 1,356,797 SNPs are all bi-allelic...
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