I am having SNP data of RIL populations and the Phenotypic data. Now I want to construct the linkage map using JoinMap. As I have no expertise of join map it would be nice if someone could provide a step by step procedure which I should follow. Thank you for giving valuable inputs in advance.
First of all, you should have both parents associated with SNPs and your F2 or other advance population data in excel file. After that you have change make format that is called ABH format and it will be converted in join Map format using VB codes on excel sheet. In the end, this Jon map formatted data will be saved on textpad in .loc path. Once you file is ready, you can load this file in JoinMap software. If you have any query related to this software, let me know and I will help you out.
Thanks
Anuj Kumar
we have done it up to this time. which LOD should i use for prteapearing Linkage group
How can we add our phynotypic data so that we may get SNP coseggregating with the trait i am interested in
You should choose LOD value more than 3.0 because less than 3 is not good for linkage maps. Second question, all data should be together means your phenotypic and genotypic data.
If you want to make any association with your phenotypic data and genotypic data, you can use TASSEL and GAPIT(Genome Association and prediction Integrated Tool). These tools will give you better results and images for your higher publications.
Thanks
Anuj kumar
Thanks for your answers. I will Try TASSEL and GAPIT as I have Phenotypic data (resistant gene) of 132 RIL population. If I face any problem will get back to you
Don`t waste your time for TASSEL and GAPIT. They are for genome association mapping. You should use mapQTL or Qgene for QTL mapping. If you want to map single gene, you should use joinMAP.
Dear Mr. Kumar,
From your first answer that included converting the data to the ABH format, a question comes to my mind which is: If I have population without parents, how can I generate ABH format? in other words, my population came from self-cross and it does not have parents because, simply, it is wild plant; what is the principle that I should follow to change the SNP data to ABH format?
I would be thankful if you or anyone can help me.
regards
Hayba
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