User: Shicheng Guo

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Shicheng Guo5.0k
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Posts by Shicheng Guo

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Answer: A: Ancestry Informative Markers
... Ancestry Informative Markers African American vs European Ancestry We selected a grid of 3,388 markers (distributed approximately one per megabase, across the autosomes and the X chromosome) that showed strong differentiation between African- and European-ancestry samples sequenced by the 1000 Geno ...
written 1 day ago by Shicheng Guo5.0k
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Comment: C: Convert multi-allele to bi-allele
... In my opinion, we can separate these multi-allelic variants and do the association separately with specific statistic method. ...
written 1 day ago by Shicheng Guo5.0k
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Comment: C: How do I remove duplicated by position SNPs using PLink?
... Here, you might be have a bug. When there is duplicated SNP with same ID, --exclude will remove all the SNPs simultaneously. If you want to --exclude, be sure to change the ID name to different one advanced. ...
written 2 days ago by Shicheng Guo5.0k
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IHEC metadata to Tab separate structured data
... Hi All, I want to do some further analysis based on IHEC methylation data. However, after I download the metadata, I don’t know how to read it. How to turn metadata to structured excel or tab separated tables? The metadata link: http://epigenomesportal.ca/cgi-bin/api/getDataHub.py?session=8298 ...
metadata ihec tab written 7 days ago by Shicheng Guo5.0k
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Comment: C: CpG-SNPs for newbies
... check the nucleotide after SNPs with 'C' and the nucleotide before SNPs with 'G', then you can identify all these CpG-SNPs. Later I will do the genome-wide analysis and provide a full list of CpG-SNP ...
written 25 days ago by Shicheng Guo5.0k
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Answer: A: Haplogroup Prediction
... Please check this database to find your answer: https://isogg.org/tree/ ...
written 4 weeks ago by Shicheng Guo5.0k
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Answer: A: Maternal and Paternal Haplogroups Assignment Package
... Done. Find the hash key: https://genome.cshlp.org/content/12/2/339/suppl/DC1 and the project main page: https://isogg.org/tree/ ...
written 4 weeks ago by Shicheng Guo5.0k
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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 12 weeks ago by Shicheng Guo5.0k
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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 12 weeks ago by Shicheng Guo5.0k
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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 3 months ago by Shicheng Guo5.0k

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