User: dirranrak
dirranrak • 10
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Posts by dirranrak
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A: Recoding plink file from 12 to 01
... Hi, sorry for not giving enough details. I am trying to use finestructure, I need chromopainter file to be able to work with. I have plink ped file recoded 12, I need to convert the plink file into chromopainter format by using plink2chromopainter.pl. I followed the instruction from the finestructur ...
written 2.1 years ago by
dirranrak • 10
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... Hi all,
I tried to use Plink2chromopainter.pl to convert plink file to chromopainter file. I have plink file recoded 12 but I need to recode the file to 01 before using the program. I did use --recode 01 --output-missing-genoty 3. I have red the plink manual but I still got a strange content in the ...
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... Thank you Jean-Karim Heriche, the cluster itself solved the problem, I did not do something wrong apparently. Might be something wrong within the system. Thank you very much ...
written 3.6 years ago by
dirranrak • 10
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... Hi all,
I am trying to estimate the lowest CV by using what is in page 4 of the manual. It is working well when I use the script on my local computer. But when I try to submit a job on the cluster, the cluster accepts only the very basic script which "./admixture file K" however, it does not accep ...
written 3.6 years ago by
dirranrak • 10
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... Hi all,
I tried to convert Plink file to Treemix file, I remarked that in the note at different websites you need to get a .frq file from using --freq --within flag in Plink. But the thing is that when you use the these flags in the same run, you get a .frq.strat file but not only .frq. I followed ...
written 3.6 years ago by
dirranrak • 10
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... Hi chrchang523,
Thank you for your answer. Does it mean that it is no need to test the quality of the merged dataset? and what should be the best way to minimize bias? ...
written 3.7 years ago by
dirranrak • 10
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... Hi all,
After filtering and merging data from using --bmerge flag in Plink 1.9, I did use the same thresholds as before merging the dataset to test the quality of the merged dataset. Then I have this "error: All people removed due to missing genotype data (--mind)". Why I loose the quality that I h ...
written 3.7 years ago by
dirranrak • 10
• updated
3.7 years ago by
chrchang523 ♦ 6.4k
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... Hello all,
I have convert plink file ped and map to eigenstrat file using convertf to be used on ALDER. When I run the converted files, I got fatalx: no real map. I don't know if it is related to make fail error when compiling the program. I installed FFTW3 and LAPACK as required but I don't unders ...
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... Hi Zev,
Thank you for the code. I was busy to understand learning coding other stuff. But now when I try to run your code in R, even just at the beginning I got the error below. And if I remove the quote when specifying the directory, the rest of the code becomes comment.
plot.admixture<-f ...
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... Hi all,
I have some genotype datasets from Illumina and Affymetrix, I am a bit confused because I still have an abnormal pca plot after merging the data using --bmerge with plink. They are in ATGC allele.
What I did: get the Pan Asian dataset (Affymetrix 50k_Xba Gene chip), recode the 0,1,2,9 alle ...
written 3.8 years ago by
dirranrak • 10
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