User: kelly.wang135

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Korea, Republic Of
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21 hours ago
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1 year, 8 months ago
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Posts by kelly.wang135

<prev • 16 results • page 1 of 2 • next >
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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 10 days ago by kelly.wang13520
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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 3 months ago by kelly.wang13520
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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 3 months ago by kelly.wang13520
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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 3 months ago by kelly.wang13520 • updated 3 months ago by Pierre Lindenbaum96k
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Comment: C: Extract several fields from vcf file
... Thanks, but I am looking for tools to handle this. ...
written 3 months ago by kelly.wang13520
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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 3 months ago by kelly.wang13520
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Extract several fields from vcf file
... Hello all, I'd like to modify my vcfs to contain several info only. There are "GT:AD:DP:FT:GQ:PL:PP" in format column, but I want to include "GT,DP,GQ" only. I ran "--extract-FORMAT-info" of vcftools, but the result file is not vcf format. What I want to have finally, is vcf file with "GT,DP,GQ" fi ...
vcf written 3 months ago by kelly.wang13520 • updated 12 weeks ago by Len Trigg810
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GTEx RNA sequencing data in RPKM
... Hi, I am new to RNA-sequencing data and have one question regarding normalization. I could download RNA-sequencing data in both read counts and rpkm. I thought I could use rpkm for eQTL analysis but little confused because there was this sentence on the following page of GTEx website. "The RPKM va ...
rpkm gtex rna-seq normalization written 4 months ago by kelly.wang13520
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TCGA whole genome sequencing data
... Hi all, I am now analyzing TCGA data and have been approved for data access. I am interested in germline mutation from whole genome sequencing data and could download vcf files by individual sample. But there were only several hundreds of variants in one vcf file per sample (smaller number than I ...
tcga written 4 months ago by kelly.wang13520
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Comment: C: TCGA genotype data
... Thanks, so they were moved to archive. Actually, it will be better to use sequencing data of blood samples in vcf fomat. But when I chose "SNV" fot Data Category, it returned only "somatic mutations" files. So I thought I should use array-based genotype files! But when I downloaded these "Annotated ...
written 5 months ago by kelly.wang13520

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