User: mostafarafiepour
mostafarafiepour • 80
- Reputation:
- 80
- Status:
- Trusted
- Location:
- Last seen:
- 2 days, 15 hours ago
- Joined:
- 2 years, 9 months ago
- Email:
- m***************@yahoo.com
Posts by mostafarafiepour
<prev
• 165 results •
page 1 of 17 •
next >
0
votes
0
answers
89
views
0
answers
Comment:
C: Open files created with bwa
... Exactly these three files (bwt, pac, sa) will not open. ...
written 2 days ago by
mostafarafiepour • 80
0
votes
0
answers
89
views
0
answers
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
mostafarafiepour • 80
0
votes
0
answers
89
views
0
answers
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
mostafarafiepour • 80
0
votes
0
answers
89
views
0
answers
... 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 days ago by
mostafarafiepour • 80
0
votes
0
answers
234
views
0
answers
... 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 11 months ago by
mostafarafiepour • 80
0
votes
1
answer
410
views
1
answer
... 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 16 months ago by
mostafarafiepour • 80
0
votes
0
answers
2.0k
views
0
answers
... 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
mostafarafiepour • 80
1
vote
0
answers
2.0k
views
5 follow
0
answers
... 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 16 months ago by
mostafarafiepour • 80
• updated
12 months ago by
ginushika • 0
1
vote
0
answers
793
views
0
answers
... 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 22 months ago by
mostafarafiepour • 80
0
votes
1
answer
1.1k
views
1
answers
Comment:
C: Create a 3-D PCA
... Many thanks dear cpad0112 for your good advice. ...
written 23 months ago by
mostafarafiepour • 80
Latest awards to mostafarafiepour
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Common SNPs among all populations
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Size difference between Bam file and sort-bam file
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Count number of SNPs per chromosome in vcf file
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Break the VCF file into the chromosome
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 VEP- What is the best idea to start analyzing?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Combine the fastq files
Popular Question
11 months ago,
created a question with more than 1,000 views.
For What is the difference between HaplotypeCaller and UnifiedGenotyper?
Popular Question
11 months ago,
created a question with more than 1,000 views.
For VEP- What is the best idea to start analyzing?
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
Popular Question
16 months ago,
created a question with more than 1,000 views.
For Size difference between Bam file and sort-bam file
Popular Question
16 months ago,
created a question with more than 1,000 views.
For VEP- What is the best idea to start analyzing?
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
Popular Question
22 months ago,
created a question with more than 1,000 views.
For How to phase a vcf file
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Replacing a values from a column in another column
Centurion
2.1 years ago,
created 100 posts.
Rising Star
2.6 years ago,
created 50 posts within first three months of joining.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1852 users visited in the last hour