User: janeshen91

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janeshen910
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Posts by janeshen91

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Using genecluster program on 1000 genome data
... I've recently learned about the gene cluster program, and am intrigued on what it would do on my set of GWAS data. I've noticed that they stopped supporting it but I'm wondering if it's possible to run it using the 1000 genome data as reference? Specifically, it seems like I'm missing a tree file. H ...
gwas snp written 4.9 years ago by janeshen910 • updated 4.9 years ago by Biostar ♦♦ 20
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Comment: C: SmartPCA gives very different PCs for different chromosomes
... Thanks. I did LD pruning and I am interested in the local population structure in europe. You might be right in that the problem might be in the maf threshold is set too low. ...
written 5.0 years ago by janeshen910 • updated 13 months ago by _r_am32k
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SmartPCA gives very different PCs for different chromosomes
... I'm using 1000 genome data on European populations. I know there should be some population structure, but smartpca (from eigensoft version 6) gives very different PCs and eigenvalues for each of the 22 chromosomes. By this I mean if I look at the PCA plots, they look very different (some are really ...
latest written 5.0 years ago by janeshen910
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encode project .bb annotation files
... I've been looking at ENCODE's annotation files such as the one below https://www.encodeproject.org/documents/46933bb0-e974-4976-87e9-aa671046d106/@@download/attachment/ENCODEElementsprototypeREADME.pdf It seems to be a good resource, as it combines multiple types of data (chipseq, DNase HS) across ...
encode epigenome roadmap written 5.7 years ago by janeshen910 • updated 5.7 years ago by PoGibas4.8k

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