User: mostafarafiepour

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Posts by mostafarafiepour

<prev • 165 results • page 1 of 17 • next >
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Comment: C: Open files created with bwa
... Exactly these three files (bwt, pac, sa) will not open. ...
written 2 days ago by mostafarafiepour80
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Comment: C: Open files created with bwa
... I asked you to provide a solution to open these files, not to comment on the contents. ...
written 2 days ago by mostafarafiepour80
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Comment: C: Open files created with bwa
... I want to see what structurally indexed files are different from genome references? ![enter image description here][1] [1]: https://ibb.co/hC973j4 ...
written 3 days ago by mostafarafiepour80
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Open files created with bwa
... Hi All, I indexed the human reference genome using bwa software (bwa index option) And the following files were created for me: GCF_000001405.39_GRCh38.p13_genomic.fna.bwt GCF_000001405.39_GRCh38.p13_genomic.fna.pac GCF_000001405.39_GRCh38.p13_genomic.fna.amb GCF_000001405.39_GRCh3 ...
bwa written 3 days ago by mostafarafiepour80
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calculate fst for every allele in any position
... Hi Dear all, I have a table of SNPs with alleles in any position (alleles A1 and A2) (As you can see in the table below). So, I want to calculate the Fst for each position. I can only calculate Fct for the VCF file but I have no idea about it. What is the best idea? SNP Chr Posi ...
fst snp written 11 months ago by mostafarafiepour80
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Separating a region of the VCF file
... Hi Dear All, I'm trying to separate 5Mb to 10Mb region of my VCF file with vcftools. But when I get the output, it only contains a header?? What is the best idea? Codes I run: vcftools --vcf My_Chr20.vcf --chr 20 --from-bp 5000000 --to-bp 10000000 --recode --out My_Output or ...
vcftools snp written 16 months ago by mostafarafiepour80
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Comment: C: Calculate Fis (inbreeding coefficient)
... Hi Ram, Many thanks for your reply, please see here (https://www.biostars.org/p/266502/) for your first question. I mean by "Fis for population": You said that (plink also has a way to compute inbreeding coefficients, but again, they are done at the individual level), Right? So, my question is, ca ...
written 16 months ago by mostafarafiepour80
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Calculate Fis (inbreeding coefficient)
... Hi Dear, I want to calculate Fis (inbreeding coefficient) for each population (I have a VCF file for each population and my data is whol genome sequencing). After my online search, I came to the conclusion that I have to use the following code to calculate Fis: vcftools --vcf my_vcf --het --ou ...
vcftools snp written 16 months ago by mostafarafiepour80 • updated 12 months ago by ginushika0
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Calculate heterozygosity for each SNPs in the bim file.
... Hi all dear, I have downloaded a database that is related to SNP-chip data. This database contains three files: ![enter image description here][1] So, i want to Calculate heterozygosity for each SNPs. I use plink --make-bed --file Colli_buffalo_diversity --freqx --out Coli_freqx script to calcul ...
snp-chip snp written 22 months ago by mostafarafiepour80
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Comment: C: Create a 3-D PCA
... Many thanks dear cpad0112 for your good advice. ...
written 23 months ago by mostafarafiepour80

Latest awards to mostafarafiepour

Popular Question 11 months ago, created a question with more than 1,000 views. For Common SNPs among all populations
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Popular Question 11 months ago, created a question with more than 1,000 views. For How Can I Count Snps In My Final Vcf Files
Popular Question 11 months ago, created a question with more than 1,000 views. For Size difference between Bam file and sort-bam file
Epic Question 16 months ago, created a question with more than 10,000 views. For Replacing a values from a column in another column
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Popular Question 16 months ago, created a question with more than 1,000 views. For Count number of SNPs per chromosome in vcf file
Popular Question 16 months ago, created a question with more than 1,000 views. For How Can I Count Snps In My Final Vcf Files
Popular Question 16 months ago, created a question with more than 1,000 views. For Size difference between Bam file and sort-bam file
Great Question 22 months ago, created a question with more than 5,000 views. For Replacing a values from a column in another column
Popular Question 22 months ago, created a question with more than 1,000 views. For Size difference between Bam file and sort-bam file
Popular Question 22 months ago, created a question with more than 1,000 views. For Count number of SNPs per chromosome in vcf file
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