User: mostafarafiepour
mostafarafiepour • 110
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Posts by mostafarafiepour
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C: Open files created with bwa
... Exactly these three files (bwt, pac, sa) will not open. ...
written 3 months ago by
mostafarafiepour • 110
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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 3 months ago by
mostafarafiepour • 110
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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 months ago by
mostafarafiepour • 110
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... 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 ...
written 3 months ago by
mostafarafiepour • 110
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... 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 ...
written 15 months ago by
mostafarafiepour • 110
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... 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
...
written 19 months ago by
mostafarafiepour • 110
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... 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 20 months ago by
mostafarafiepour • 110
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... 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 ...
written 20 months ago by
mostafarafiepour • 110
• updated
15 months ago by
ginushika • 0
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... 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 ...
written 2.2 years ago by
mostafarafiepour • 110
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1.3k
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Comment:
C: Create a 3-D PCA
... Many thanks dear cpad0112 for your good advice. ...
written 2.2 years ago by
mostafarafiepour • 110
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