User: Siavash Salek Ardestani
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- 1 day, 3 hours ago
- Joined:
- 2 years, 6 months ago
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Posts by Siavash Salek Ardestani
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... Hello,
I am trying to prepare a list for the public (downloadable) simulated SNP dataset. Would you please inform me here if you know any public simulated SNP dataset?
Thanks,
Siavash ...
written 3 months ago by
Siavash Salek Ardestani • 20
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... Hi,
I calculated the Fst values (through Weir and Cockerham by a sliding-window approach in VCFtools) between two populations with different sample sizes (pop1=32 , pop2=14). I want to know, how can I adjust the Fst values to correct for sample size??
...
written 5 months ago by
Siavash Salek Ardestani • 20
• updated
5 months ago by
Fabio Marroni • 2.6k
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... Hello,
I am working on a signature of selection study. I want to know, is there a software In order to calculate the pooled heterozygosity (Hp) score using a sliding window approach (100 kb with a step size of 50 kb)?
My SNP data format is variant call format (VCF).
Thanks ...
written 13 months ago by
Siavash Salek Ardestani • 20
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Dear finswimmer,
In this data first column is included samples (A,B,C,etc), the second column is included genotypes (each number per SNP). So, I need to know, for example, how can I extract A B C samples and their genotypes together (all data in A B C rows) in a text file.
...
written 20 months ago by
Siavash Salek Ardestani • 20
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... No, my data format is not VCF. ...
written 20 months ago by
Siavash Salek Ardestani • 20
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... Dear finswimmer,
Actually, it is a small example and my real data is much bigger than this dataset. The format is text (txt). Here the first column is included the individuals and the second column is their genotypes. I want extract the"A","B" and "C" genotypes in text file like this:
A 1111212 ...
written 20 months ago by
Siavash Salek Ardestani • 20
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... How can extract these individuals "A", "B", "C" and their genotypes in this dataset?
Is there a command in linux for this?
A 11112121112121121102111121110
B 11211112112110211111211121110
C 20222222202020220202222222220
D 11111112112110211111211121110
E 20222222202020220202222222 ...
written 20 months ago by
Siavash Salek Ardestani • 20
• updated
20 months ago by
paolo002 • 160
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... Hi,
I have many coordinates (approximatly1000), I want to know how can I find the gene symbols that are in these coordinates?
Thanks,
Siavash ...
written 2.2 years ago by
Siavash Salek Ardestani • 20
• updated
2.2 years ago by
Alex Reynolds ♦ 30k
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... Hi to all, I have a vcf file that including multisample. I want to calculate expected heterozygosity for this vcf file by sliding-window approach(40-kb-windows slidingin20-kb-steps).
I want to know, which software do this?
Thanks,
Siavash ...
written 2.2 years ago by
Siavash Salek Ardestani • 20
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... Hi
Thank you for useful comment. Yes of course, I did it.
The best,
Siavash ...
written 2.3 years ago by
Siavash Salek Ardestani • 20
Latest awards to Siavash Salek Ardestani
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created a question with more than 1,000 views.
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For SNP,INDEL counting per chromosomes in vcf
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For SNP,INDEL counting per chromosomes in vcf
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