User: miaowzai

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miaowzai50
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50
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Location:
United States
Last seen:
23 hours ago
Joined:
2 years, 11 months ago
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m*******@gmail.com

Posts by miaowzai

<prev • 23 results • page 1 of 3 • next >
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Comment: C: strand information for SNPs from VCF file (convert into IMPUTE format)
... I found a tool to do this: https://github.com/biocore-ntnu/snpflip ...
written 8 weeks ago by miaowzai50
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Comment: C: Illumina exome beadchip duplicated positions
... This makes a lot of sense! Thank you so much. ...
written 8 weeks ago by miaowzai50
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Illumina exome beadchip duplicated positions
... I have a plink format data (bim/bed/fam) from data provider. As far as I know, the sequencing was done by Illumina exome SNP beadchip. I didn't call the genotypes. There are some variant IDs startwith "exm". They do have rs numbers when I look'em up. What are these SNPs? Why use "exm"? Also, I fou ...
exome illumina snp beadchip written 8 weeks ago by miaowzai50
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Comment: C: Error running smartpca from eigensoft
... I searched and there're one or two exact same questions on biostars as well without any answers. I checked my $PATH and the smartpca bin folder is in my $PATH, and it still doesn't work. So I've come up with a barbarian way to do it (answered below) and now it is running. ...
written 9 weeks ago by miaowzai50
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Answer: A: Error running smartpca from eigensoft
... I have the exact same problem with Rilquer and setting the $PATH didn't help (I don't know why, very strange). I couldn't run the example.perl file, either. There is a very barbarian way to solve it. Go to your smartpca.perl file and change the `system(...)` calls. There're not many of them, only t ...
written 10 weeks ago by miaowzai50
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Comment: C: Error running smartpca from eigensoft
... I have the exact same problem. I also set the bin folder into my $PATH but that didn't help. ...
written 10 weeks ago by miaowzai50
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Comment: C: Error running smartpca from eigensoft
... I have the exact same problem with Rilquer. I understand that doing it separately would help, but I didn't understand the code in your answer. Could you please explain a little bit more about how to do this separately? Thank you so much. ...
written 10 weeks ago by miaowzai50
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Answer: A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
... bgzip file.vcf # or: bcftools view file.vcf -Oz -o file.vcf.gz tabix file.vcf.gz # or: bcftools index file.vcf.gz this is convenient where tabix and bgzip are not installed. saw this from: https://github.com/samtools/bcftools/issues/668 ...
written 3 months ago by miaowzai50
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strand info of array chips
... I'm trying to understand the strand info provided by this site: http://www.well.ox.ac.uk/~wrayner/strand/ I downloaded the InfiniumOmniExpress-24v1-2_A1-b37-strand file. In the .strand file, for example, there is a SNP rs11202902 at chr10:90693537, the strand column says “-“ and the alleles column ...
chip-seq microarray strand written 9 months ago by miaowzai50
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Comment: C: what is 0 in the plink .bim file under allele1/2 column?
... May I ask why this happens? Thanks! ...
written 9 months ago by miaowzai50

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