User: mike229lin

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mike229lin10
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m*********@gapp.nthu.edu.tw

Posts by mike229lin

<prev • 13 results • page 1 of 2 • next >
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the function of readVCF in PopGenome R package
... Hello I'm using PopGenome R package to calculate Fst with vcf files. I met some problems during the protocol First, I want to analyze whole genome level data. In the manual of PopGenome, it says I should input a specific chromosome or scaffold name. If I want to generate Fst of whole genome, what ...
vcf R popgenome fst written 9 months ago by mike229lin10 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: Which method to calculate pairwise Fst from SNP data
... Use STACKs http://catchenlab.life.illinois.edu/stacks/ ...
written 9 months ago by mike229lin10
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Comment: C: VCF filtering by depth
... you should try --min-meanDP instead of --minDP if you didn't solve that problem. I'm also wondering why vcftools write some argument making user a little bit confusing. Like --min-meanDP & --minDP or --minQ and --minGQ ...
written 10 months ago by mike229lin10
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Comment: C: Error: --fst requires at least two nonempty clusters.
... Does anyone think that the manual of PLINK is not easy to understand? ...
written 12 months ago by mike229lin10
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Comment: C: Subset analyze of multiple sample file in PLINK 1.9
... I have tried the --keep mylist_location.txt in my command But it shows Error: Line 1 of --keep file has fewer tokens than expected. the format in mylist_location1.txt looks like sample1 sample2 sample3 sample4 but it shows Error in the end ...
written 12 months ago by mike229lin10
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Comment: C: Subset analyze of multiple sample file in PLINK 1.9
... Besides that How about using > --within [filename] ? I want to know how to use clusters of samples, but I don't quite understand the format of cluster file ...
written 12 months ago by mike229lin10
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Comment: C: Subset analyze of multiple sample file in PLINK 1.9
... Thanks for your help So, the command > `plink --file data --keep mylist_location1.txt` means that PLINK generate the binary files with the list from my input data? the command may look like `plink --file data --keep mylist_location1.txt --make-bed --out output.binary`? or means I can only us ...
written 12 months ago by mike229lin10
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Subset analyze of multiple sample file in PLINK 1.9
... Hello, I want to do GWAS with PLINK. I already have a data containing all the samples and have done association analyze with plink command below. plink --bfile All_SNP.binary --make-pheno phenotype.pheno "phenoA" --aec --assoc --reference-allele All_alt_alleles --allow-no-sex --adjust --nowe ...
sequence plink snp written 12 months ago by mike229lin10 • updated 12 months ago by zx87547.9k
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Short Variants calling error when using bcftools mpileup
... Hello, I want to call gvcf with bcftools mpileup containing variant site and reference homologous site blocks The command line shows below nohup sh -c "bcftools mpileup -C50 -q25 -g 4 -t DP -f reference.fa sample.bam | bcftools call -c | vcfutils.pl varFilter -d4 -D28 > output.g.vcf" & ...
genome alignment snp written 12 months ago by mike229lin10 • updated 12 months ago by finswimmer12k
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Comment: C: Cannot locate the Vcf.pm every time I logging on the server
... It works ! thanks for help ...
written 12 months ago by mike229lin10

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