User: kelly.wang135

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Korea, Republic Of
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1 month ago
Joined:
1 year, 10 months ago
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Posts by kelly.wang135

<prev • 20 results • page 1 of 2 • next >
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Comment: C: Homozygous exonic markers from AI analysis
... Thank you. If there are only homozygous SNPs for the exons of this gene, I should conclude 1) ase analysis cannot be done with this data, or 2) there is no association between this marker SNP and the expression of gene? ...
written 5 weeks ago by kelly.wang13530
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Comment: C: Homozygous exonic markers from AI analysis
... Are you asking for thr marker SNP? Marker SNPs are AA, AB or BB, and exonic SNPs are almost all homozygous regardless of marker SNP. ...
written 5 weeks ago by kelly.wang13530
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Comment: C: Homozygous exonic markers from AI analysis
... Yes to both questions. Exonic SNPs are used to represent expression of that gene and expression can be assessed through RNA-seq. AI is calculated as max (ref, alt) / ref+alt where ref and alt mean the number of ref or alt alleles. So AI=1 means homozygous alleles. Thanks! ...
written 5 weeks ago by kelly.wang13530
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Homozygous exonic markers from AI analysis
... Hi, I am doing allelic imbalance analysis (or allele-specific expression analysis) and have a question. I want to see the association between marker SNP and nearby exon SNPs. My data shows that for all three types of status of marker SNP (AA, AB, BB), AI ratios of exon SNPs are all nearly 1. So, ...
allelic imbalance ai ase written 5 weeks ago by kelly.wang13530
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Haplotype reconstruction without genetic map
... Hi all, I am interested in haplotype reconstruction, but every software for haplotype analyses I've found requires genetic map as input (or they need pre-phasing step which also requires a genetic map file). My data is not from usual genetic build version, so genetic position for my data is not av ...
haplotype genetic map written 9 weeks ago by kelly.wang13530
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Comment: C: Convert multi-allele to bi-allele
... For those sites, I want to just remove them. But for indels, multi-alleles are not caused by noises. So I want to include these sites to association test and I need to simplify them first. Actually I made it with python, but there was something wrong with new vcf file. It seems these newly D/I code ...
written 5 months ago by kelly.wang13530
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Comment: C: Convert multi-allele to bi-allele
... Thank you. But I don't want to split these sites into multiple sites. I want the number of lines remain same as before. What I want to do finally is association test, but the association tool will handle these multiple variants as independent, though they are actually from same position. So the res ...
written 5 months ago by kelly.wang13530
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Convert multi-allele to bi-allele
... Hi all, I have a vcf file and several positions have multi-allele like REF=TTT ALT=T,TT,TTTT,TTTTT To my knowledge, rare variant association tools only handle bi-allele sites. But I want to include these positions, too. So I tried to convert these sites into bi-allelic sites like "ins/del". I u ...
vcf written 5 months ago by kelly.wang13530 • updated 5 months ago by Pierre Lindenbaum99k
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Comment: C: Extract several fields from vcf file
... Thanks, but I am looking for tools to handle this. ...
written 5 months ago by kelly.wang13530
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Comment: C: Extract several fields from vcf file
... Actually I extracted these fields with python. But when I tried to analyze this file using rare variant association tool like pseq, vtools, and rvtest, something is not working properly. I wonder it there are validated tools to extract, not with linux or python. ...
written 5 months ago by kelly.wang13530

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For Where can I get exome vcf file from the 1000 genome project?

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