Activity for Lep-MAP2
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Xochitl Granados modified a comment on discussion General Discussion
Hi Pasi, I don’t understand where the pedigree file comes from, I have GBS data and I used STACKS to get files .vcf, .ped and .map but I don’t know how to get the pedigree file. In addition, I have doubts about how should be configured the pedigree file because my populations are haploid and from strictly maternal inheritance. I read in an article that the pedigree file should be configured as follows: maternal genotype to 1/2, the paternal genotype to 1/1, and missing genotype to 0/0, is correct?...
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Hi Pasi, I don’t understand where the pedigree file comes from, I have GBS data and I used STACKS to get files .vcf, .ped and .map but I don’t know how to get the pedigree file. In addition, I have doubts about how should be configured the pedigree file because my populations are haploid and from strictly maternal inheritance. I read in an article that the pedigree file should be configured as follows: maternal genotype to 1/2, the paternal genotype to 1/1, and missing genotype to 0/0, is correct?...
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Pasi Rastas posted a comment on discussion General Discussion
Dear all, Please note that I do not check this Lep-MAP2 discussion very often. Please send your question to the Lep-MAP3 discussion instead. Thank you. Cheers, Pasi
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Dear Natália, Sorry for long time to reply. Could you please post your question to Lep-MAP3 discussion, thank you. Cheers, Pasi
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Natália Mendes posted a comment on discussion General Discussion
Dear Pasi, I have three questions for you: 1) In module # JoinSingles2All which command should I use to display the amount of markers in each LG? I have used the same command as showed in # SeparateChromosomes2, but didnt work -> sort -n -r filename | uniq -c | tail -n 30 2) Which command could I use to build a consensus map for females and males? I tried using the command informativeMask = 3 in #OrderMarkers2, but in the output file .txt continued to leave the position in cM in both male and female....
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Yuqing Jin posted a comment on discussion General Discussion
Hi Pasi, It is benefit a lot to go through the discussion. I am still confused by the argument minError and the outut result Likelihoods and the value of COUNT. For example, when I set the minError=0.01, I got a very long LG length, such as 4000cM , but the Likelihood is -2000, the value of COUNT is 1900. when I set minError=0.3, I got a short LG length, such as 1000cM , but the Likelihood is -12,000, the value of COUNT is 3400. I went through what you talked before, I known that the minError can...
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Dear Gaurab, Q1. Phenotypes are not currently used for anything. Q2. Most reliable single parent maps you get by providing informativeMask=1 and informativeMask=2 separately. I have also made maps with informativeMask 13 and 23 as well. Most likely it suffices to set this parameter of OrderMarkers2 only. Q3. Indels should work as SNPs. Q4. If I understand the double pseudo test-cross correctly, it should work as F2 in LM3. Cheers, Pasi
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Gaurab Bhattarai posted a comment on discussion General Discussion
Dear Pasi, Sorry for the late reply. I solved the ped problem by simply removing that long single column and pasting data from sex column (then I replaced sex values 1 and 2 of both parents as '0' for phenotype value.(Bolded here to indicate) 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE 588160:MERGE CHR POS 1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
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Dear Gaurab, The pedigree does not seem correct. I ran the command on you example in the first post and got a correct file. Do your file has more than one space between values? Maybe you can try this then. Or just sen the pedigree (ped_lep_map_352.txt) to me so I will figure this out. sed -e 's/ [ ]*/\t/g' ped_lep_map_352.txt |./transpose_tab|awk '{print "CHR\tPOS\t" $0}' >ped_t.txt Cheers, Pasi
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Dear Pasi, Thank you so much. Yes, I realized that I forgot to give that space. I transposed the pedigree file but when I ran ParentCall2, I got this error: ~/Desktop/GBS/LepMap$ java -cp ./bin ParentCall2 data=pedigree_transposed.txt vcfFile=Beagle_imputed_phased.vcf removeNonInformative=1 >outputcall.call No grandparents present in family GB Number of individuals = 352 Number of families = 1 Error 503 Error: Wrong number of columns in the input file Note: this is my F1 population with unknown grandparents....
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Dear Gaurab, Please use the command exactly as here. I think you don't have space in sed and are missing transpose. sed -e 's/ /\t/g' ped_lep_map_352.txt |./transpose_tab|awk '{print "CHR\tPOS\t" $0}' >ped_t.txt Cheers, Pasi
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Dear Pasi and Saurav, I am trying to use LepMap-3 to generate linkage maps. To use in ParentCall2 module, I tried to transpose pedigree file (.txt) first. But it shows following error: sed -e 's//\t/g' ped_lep_map_352.txt awk '{print "CHR\tPOS\t" $0}' >ped_transposed.txt sed: -e expression #1, char 0: no previous regular expression I do have my ped file format as follows: GB 588160:MERGE 0 0 2 1 GB 588271:MERGE 0 0 1 1 GB 160_271_001:C7TMYANXX:6:250514961 588271:MERGE 588160:MERGE 0 1 GB 160_271_002:C7TMYANXX:6:250514962...
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Dear krishna, I am creating a new thread for this in LM3 forum. https://sourceforge.net/p/lep-map3/discussion/general/thread/11f56293/#627d Cheers, Pasi
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Dear krishna, I am creating a new thread for this in LM3 forum. Cheers, Pasi
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krishna posted a comment on discussion General Discussion
Two more questions: 3) If we have PL or GL field in VCF file, would it be automatically included in the analysis by LM3 or we must make a separate ped file with PL info ? 4) how to make a ped file with posteriors (from PL) for LM3. Right now my ped file does not contain posterior info.
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Dear All, 1) If the sex of offsprings in a family is not available can I set it to 0 in the ped file , while I set FATHER to 1 and MOTHER to 2 2) Is there a way to visualize ordered markers into graphical format like genetic map of LGs seen in publications. I understand we can convert ordered markers of a given chromsome into dot file but that doesnt appear like standard LG image.
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Dear Jose, Sorry for taking time to aswer. I only rarely visit Lep-MAP2 discussion anymore. The problem is in you command, just remove "chromosome_map_file=" from the command, i.e. java -cp bin/ JoinSingles paternal_LOD5_30Jan18.txt .... Cheers, Pasi
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Jose Andres posted a comment on discussion General Discussion
Hi there, I have managed to group my markers into LGs and I now want to "join singles" but my JoinSingles command line cannot upload the map file (SeparateChromosomes output). The map file is in the directory from which I am running the module and I can open it with my text editor. See pasted. Any suggestions? Thanks dhcp-ccc-5161:LepMap2_binary_and_code Jose$ ls COPYING bin paternal_separateChromosomes_30June18 LDmap_with_Joinsingles_LOD5_30Jan18 bothparents_separateChromosomes_30June18_LOD10 paternal_separateChromosomes_30June182...
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Dear Homa. Sorry, for taking time to answer. I have not been checking Lep-MAP2 discussion lately (Lep-MAP3 is currently my main focus). It is very difficult to say exactly what is happening here without more detailed information. However, the 2-point analysis is not necessary showing all recombinations, as there can be missing genotypes in one or both markers. For this reason, Lep-MAP2+ does not use any 2-point estimates but only multipoint likelihoods. Hope this answers yous question? Cheers, P...
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Homa posted a comment on discussion General Discussion
Dear Pasi, Lepmap integrates many more markers into the map compared to Crimap. When there is no recombination or very low amount of recombination, I see for some markers, there is some noise in calculating the genetic map location. An example is seen below for the non-recombining segment of the sex chromosome in females: chrZ 58175814 58175815 81.163 scaffold62 2446259 chrZ 58181948 58181949 79.14 scaffold62 2452393 chrZ 58182233 58182234 79.14 scaffold62 2452678 chrZ 58216972 58216973 81.163 scaffold62...
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Dear Homa, The hidden Markov model parameters in the EM algorithm are restricted to be same so that the two map positions become exactly the same. Cheers, Pasi
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Dear Pasi, Thank you very much for your response. Could you please explain a bit more what it means that it restricts the two positions to be exactly the same? In what regard they should be the same? Thanks, Cheers, Homa
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Dear Homa, Thank you for your question. Lep-MAP2 calculates sex-averaged positions using EM-type algorithm by restricting the two positions to be exactly same. This can yield different positions than averaging the two positions. You can average the male and female positions if that seems more appropriate. Cheers, Pasi
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Dear Pasi, I was wondering how Lepmap2 computes sex averaged map? For the following positions (male and female positions): 3.096 4.768 I would obtain ((3.096+4.768)/2)=3.932 as the sex averaged position However, Lepmap2 gives 5.146 as the sex averaged. This is true for other positions as well. How is it then calculated? Thank you, Homa
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Stephen Trevoy posted a comment on discussion General Discussion
Hi there, Some questions for formatting the .csv files so the R script runs properly: 1) Do chromosomes need to be separated into their own .csv files? 2) Do families need to be separated into their own .csv files?
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Dear R Sheldon, Thank you for your detailed question. My guess is that all marker are identical, that is why you get all markers collapsing into one. Does this happen on all linkage groups or only on (chromosome=) 2? By adding parameter outputPhasedData=1 LM will ouput the most likely segregation patterns. These can provide more information. With only 16 individuals, the linkage mapping does not necessary work that simply from the paternal markers. Based on the output of SeparateChromosomes and JoinSingles,...
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Sheldon89 posted a comment on discussion General Discussion
Hi Pasi and Lep-map users, I'm trying to use 4928 high quality SNPs (that were used...
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Rastas Pasi M A committed [42ad25]
Support for phased data
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Joshua Penalba posted a comment on discussion General Discussion
Hi Pasi, Thanks for the response. Glad to hear that Lep-MAP3 can handle half-sibs!...
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Dear Joshua, Thank you for sharing your pedigree. It looks a bit hairy to me:) However,...
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PS. When I say complicated, I mean it looks like this. Where the dotted lines link...
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Hi Rasi, I'm about to try LM2 for a fairly complex pedigree of a natural population...
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Dear Pasi, Thank you very much, your answer was really helpful. I will describe the...
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Jian-Feng Mao posted a comment on discussion General Discussion
Dear Pasi, Thanks for your kind reply. And sorry for our late response, as we was...
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Dear Homa, Thank you for your email and sorry for late reply. The markers withing...
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Dear Pasi, Thank you very much for your great help throughout my analyses. I have...
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Dear Jian-Feng Mao, Here are some answers about OrderMarkers. 1) The internal hidden...
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Dear Jian-Feng Mao, Thank you for your comprehensive question. I will try to anwer...
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Dear Shenfei, Thank you for your question. It is hard to say why the maps are too...
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Dear Pasi and Lep-map users, Here, we want to know your opinions on good practice...
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Dear Pasi and Lep-map users, Glad to write here. Here, we have a question on output...
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Shenfei posted a comment on discussion General Discussion
Dear Pasi Rastas, Thanks for your response，I constructed a genetic map. but I find...
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Saurav Baral posted a comment on discussion General Discussion
Dear Pasi, Thank you for your invaluable help. I think the issue was with my vcf...
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Dear Pasi, I transposed the pedigree files and did the analysis again. This time...
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Ok, The pedigree must be tranposed, my old school fix is this (ped.txt is the pedigree...
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Dear Pasi, I tried running the command as you suggested. I am getting a java error:...
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Dear Homa, Thank you for your email. I might be biased here but I answer anyway....
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Dear Saurav Baral, Thank you for your email. The simplest way might be to use ParentCall2...
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Hello, It would be really great if someone in the Linkage map community would help...
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Dear Pasi, I was asked to run the linkage analysis using CRIMAP as well as Lepmap2....
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Dear Flynn Shen, Thank you for your email. LM outputs two map positions for each...
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Dear Pasi Rastas, I try to contruct genetic map of apple tree (CP population).and...
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computeLODScores index fix
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Sean Stankowski posted a comment on discussion General Discussion
Hi Pasi, Thankyou for looking into this. I have just checked this for one LG, and...
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Dear Sean and all, I think I figured this out. The phased output of LM is not interlaced...
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Dear Sean, Your example looks a bit worrying. However, outputPhasedData=1 will output...
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Dear Pasi Thanks for your response! I have gone through the process of outputting...
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AchiasmaticMeiosis bug fix
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AchiasmaticMeiosis
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Dear Sean, Thank you for your question. The phase reported by LM (00,01,10,11) is...
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Federico Calboli posted a comment on discussion General Discussion
With SexAveraged=1 you find the average linkage map (average of the two parents)....
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Baoqing Ye posted a comment on discussion General Discussion
Thank you for the the information ! I have found out that by setting SexAveraged=1,...
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Hi Pasi, I have been using your mapping software for a while to build a high-density...
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Hi Pasi, I have been using your mapping software for a while to build a high-density...
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On 17 Oct 2016, at 09:48, Baoqing Ye yipmo@users.sf.net wrote: Dear Pasi Rastas,...
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you have 1 male and 1 female as you stated — the male and female in the results is...
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Dear Pasi Rastas, I have a related question: How do we interprete the results for...
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Dear Homa, Typically the fact that there are many markers at same positions is an...
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Dear Pasi, I was wondering how much the order of the markers that have the same map...
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Dear Homa, Plot looks quite good. It would be easier to see if you would cap the...
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Dear Pasi, Thank you very much for your reply. I followed your instructions and I...
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Dear Pasi, Thank you very much for your reply. I followed your instructions and I...
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Dear Homa, Thank you for your question. Yes this is possible. With the simulated...
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Dear Homa, Thank you for your question. Yes this is possible. With the simulated...
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Dear Pasi, It is written in the manual that the errors in marker orders can be detected...
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Matt Rockman posted a comment on discussion General Discussion
Terrific. Thanks!
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Hello Matt, Thanks for good question. Your interpretation is correct. Maternal and...
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Hi Pasi, Thanks for Lep-MAP2. It's really fantastic. It worked beautifully to put...
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Dear Sheina, Thank you for your question. Linkage groups will be split (LG1 => 1,1,...
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Hello Homa, Thank you for your email. X/ZLimit will convert sex inherited markers...
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Dear John, Thank you for this question, MinError sets the minimum error parameter...
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Hello, Thank you for the great software. I am working with the sex chromosome linkage...
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Hello, Thank you for the great software. I was wondering about two points. It would...
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Hello, Thank you for the great software. I was wondering about two points. It would...
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Hello, Thank you for the great software. I was wondering about two points. It would...
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john posted a comment on discussion General Discussion
Hi Pasi, Could you give a brief description of how the minError parameter works?...
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Hi Pasi, Yes, they do! Thank you.
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Pasi can give the technical explanation, but I understand these are two equally satisfactory...
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Sheina posted a comment on discussion General Discussion
Aloha! I used OrderMarkers and some linkage groups have additional loci under the...
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Here is the code I used, for reference. PART 1: turn LM2 output in csv files run...
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rtadmorl posted a comment on discussion General Discussion
Many thanks to you both, I will e-mail Federico.
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Dear John, Thank you for your question. The paternally informative markers include...
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Hello, Lep-MAP2 seems to not be incorporating all informative markers into my maps...
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Hi, I just wrote the code in R especially. If you email me at federico DOT calboli...
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Hi, I just worte the code in R especially. If you email me at federico DOT calboli...
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Dear John, This is a good question. Yes, the markers that have been filtered do not...
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Dear Roni Tadmor-Levi, Thank you for your question. Sorry I cannot help as I have...
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Hi Pasi, I am also interested in evaluating a specific map order. When I provide...