User: mike229lin

gravatar for mike229lin
mike229lin10
Reputation:
10
Status:
New User
Location:
Last seen:
3 months, 4 weeks ago
Joined:
1 year, 4 months ago
Email:
m*********@gapp.nthu.edu.tw

Posts by mike229lin

<prev • 13 results • page 1 of 2 • next >
0
votes
0
answers
521
views
0
answers
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 12 months ago by mike229lin10 • updated 11 months ago by Biostar ♦♦ 20
0
votes
0
answers
1.4k
views
0
answers
Comment: C: Which method to calculate pairwise Fst from SNP data
... Use STACKs http://catchenlab.life.illinois.edu/stacks/ ...
written 12 months ago by mike229lin10
0
votes
3
answers
3.4k
views
3
answers
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 13 months ago by mike229lin10
0
votes
1
answer
1.1k
views
1
answers
Comment: C: Error: --fst requires at least two nonempty clusters.
... Does anyone think that the manual of PLINK is not easy to understand? ...
written 15 months ago by mike229lin10
0
votes
1
answer
565
views
1
answers
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 15 months ago by mike229lin10
0
votes
1
answer
565
views
1
answers
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 15 months ago by mike229lin10
0
votes
1
answer
565
views
1
answers
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 15 months ago by mike229lin10
2
votes
1
answer
565
views
1
answer
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 15 months ago by mike229lin10 • updated 15 months ago by zx87548.4k
0
votes
0
answers
448
views
0
answers
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 15 months ago by mike229lin10 • updated 15 months ago by finswimmer12k
0
votes
1
answer
537
views
1
answers
Comment: C: Cannot locate the Vcf.pm every time I logging on the server
... It works ! thanks for help ...
written 15 months ago by mike229lin10

Latest awards to mike229lin

Supporter 11 months ago, voted at least 25 times.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2169 users visited in the last hour