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How the calculated the decay line by nonlinear regression to the LD plot? #10
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Dear @sekhwal By the way : A: Due to the relationship between the r2 of ld decay and the physical distance, when the Ref scaffols connected to LG, the order of the scaffols is wrong or the length of N inserted in the middle is seriously wrong, this is very likely to affect the result. Solution: In this case, you can return to the original scaffold coordinates and take the long scaffolds to analyze B: SNP of RAD or GBS sequencing or chip data may cause this situation . Solution: In this case, You can try to increase these three parameters [ -bin1 -break -bin2 ]when you draw, it will smooth your curve, like : |
the decay line fluctuation is Due to youre poor assembly ref ( Ref assembly quality is too poor ). a) PopLDdecay-3.41/bin/PopLDdecay -MaxDist 500 can make the physical distance to 500 kb Due to the relationship between the r2 of ld decay and the physical distance, when the Ref scaffols connected to LG, the order of the scaffols is wrong or the length of N inserted in the middle is seriously wrong, this is very likely to affect the result. Solution: In this case, you can return to the original scaffold coordinates and take the long scaffolds to analyze |
Hi, I am trying to add the non-linear regression tendency line to the Linkage Disequilibrium (LD) plot. I followed the manual document of PopLDdecay and got the plot. However, I am looking to make plot like above where r2 only goes until 0.5 and physical distance until 500 kb.
![Out Prefix](https://user-images.githubusercontent.com/26156590/118048830-b49eaf80-b331-11eb-8b7d-1e5a7f326ab9.png)
Got the plot using PopLDdecay.
However,
I am looking the LD plot like this with dots.
![Picture1](https://user-images.githubusercontent.com/26156590/118048813-ae103800-b331-11eb-8555-7de67bc98095.png)
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