User: Shicheng Guo

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Shicheng Guo4.8k
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Posts by Shicheng Guo

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Comment: C: Illumina exome beadchip duplicated positions
... It is caused by the allele is from different strand. GG actually == CC they are from Watson and Crick strand, respectively. Now you know the above situation, the follow situation should also be paid attention: When merging two datasets, it is clearly very important that the two sets of SNPs are ...
written 5 weeks ago by Shicheng Guo4.8k
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Comment: C: qqplot for the P-values dervided from permutation test in Plink
... Hi Kevin, How to understand the observed P-value in left figure is lower than the expectation regions? and sometimes, the observed P-values in higher than expected regions (null hypothesis). Which factors will caused the observed P-value higher or lower than the expected regions (grey region in the ...
written 5 weeks ago by Shicheng Guo4.8k
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Comment: C: Hapmap 3 in hg19/GRCh37 plink format PED and MAP
... Sorry. Format to insert the link, please download the data and related files from the following link: https://pan.baidu.com/s/1ElJ-heuW9jZXDeU9R-dZqg ...
written 6 weeks ago by Shicheng Guo4.8k
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Maternal and Paternal Haplogroups Assignment Package
... Any one share a R package or Perl package to do Maternal and Paternal Haplogroups Assignment . https://www.familytreemagazine.com/premium/top-genetic-genealogy-tools/ https://aurora-mareviv.github.io/mthapower/ Companies like 23andMe and the Geno 2.0 project provide haplogroups for both Y-line ...
haplotype haplogroup y-chromosome written 6 weeks ago by Shicheng Guo4.8k
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Comment: C: Haplogroup Prediction
... Hi, did you find the curated list. Can you share me a copy. Thanks. ...
written 6 weeks ago by Shicheng Guo4.8k
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Comment: C: clustering snps for haplogroup assignment
... Hi, did you find the curated list. Can you share me a copy. Thanks. ...
written 6 weeks ago by Shicheng Guo4.8k
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Comment: C: Is there a curated list of which snps define mitochondrial and Y-chromosome hapl
... Hi Matt, did you find the curated list. Can you share me a copy. Thanks. ...
written 6 weeks ago by Shicheng Guo4.8k
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Hash key to map Y haplotype to haplogroup
... Hi All, I hope to find a bridge to connect Y haplotype and Y haplogroup? Is there any hash key or dictionary to share with me? Thanks ...
haplotype haplogroup written 6 weeks ago by Shicheng Guo4.8k
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Comment: C: qqplot for the P-values dervided from permutation test in Plink
... Yes. Chris told me these EMP1 and EMP2 is only for genetics variants, not for covariants. If I want to show the P-values for co variants I can add --tests ...
written 7 weeks ago by Shicheng Guo4.8k
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Comment: C: qqplot for the P-values dervided from permutation test in Plink
... Hi Kevin, It's genome-wide association P-values, not selected from any chrosome. The top-right of EMP2 is my interesting SNPs. But 1) I don't understand EMP1, why they are lower in expected quantiles of P-values 2) I don't understand the relationship between EMP1 and EMP2. Also I don't understand ...
written 7 weeks ago by Shicheng Guo4.8k

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