User: shawn

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shawn20
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4 months, 3 weeks ago
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5 months ago
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Posts by shawn

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Many 0 in ped file converted from vcf genomic data
... Hi Fabio, I have adjusted the format. Thanks for your suggestion. Do you know the reason for my problem? Thank you very much. Shawn ...
written 5 months ago by shawn20
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Many 0 in ped file converted from vcf genomic data
... Hi everyone, I am learning do the gwas analysis. When I convert the genomic data "1001genomes_snp-short-indel_only_ACGTN.vcf.gz" download from [here][1] to plink ped format. plink --vcf 1001genomes_snp-short-indel_only_ACGTN.vcf.gz--make-bed --out 1001genomes_snp-short-indel_only_ACGTN.vcf.gz ...
vcf gwas plink snp written 5 months ago by shawn20 • updated 5 months ago by zx87547.8k
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Comment: C: Uncompress The 1001 Genome vcf.gz
... which dataset do you use? There are many vcf files. I do not know which one is used for gwas analysis. Thanks. ...
written 5 months ago by shawn20
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how to convert ped format to hapmap
... Hi everyone, I want to convert ped plink format to hapmap for gwas analysis. Does anyone know how to do that? Thanks a lot. ...
snp written 5 months ago by shawn20
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Comment: C: 1001 Arabidopsis SNP
... Thanks for your reply. I am not sure which dataset is the write one for 1001 project. I try to use this vcf dataset "1001genomes.org/data/GMI-MPI/releases/v3.1/1001genomes_snp-short-indel_only_ACGTN.vcf.gz". When I use plink to do the quality control " plink --bfile 387snp --maf 0.01 --geno 0.05 - ...
written 5 months ago by shawn20
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Comment: C: How Do I Convert From Bed Format To Gff Format?
... Hi Giovanni, Do you know how to convert hdf5 to plink format? ...
written 5 months ago by shawn20
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1001 Arabidopsis SNP
... Hi everyone, I am learning to do some GWAS analysis in Arabidopsis. I used some accessions from the 1135 list (1001 genomes project)for a GWAS experiment. I have some questions for the genotype data. I find there are several different genomes data including vcf format and hdf5 format. I selected ...
vcf plink snp written 5 months ago by shawn20 • updated 5 months ago by zx87547.8k

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