User: Siavash Salek Ardestani

Reputation:
20
Status:
New User
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Last seen:
1 day, 3 hours ago
Joined:
2 years, 6 months ago
Email:
s**************@yahoo.com

Posts by Siavash Salek Ardestani

<prev • 42 results • page 1 of 5 • next >
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Public simulated SNP dataset
... 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 ...
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Adjusting the Fst values for different sample sizes
... 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?? ...
population genetic fixation index fst snp written 5 months ago by Siavash Salek Ardestani20 • updated 5 months ago by Fabio Marroni2.6k
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The pooled heterozygosity (Hp) score
... 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 ...
vcf genome next-gen snp gene written 13 months ago by Siavash Salek Ardestani20
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Comment: C: Extracting sample ID and their genotypes
... 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 Ardestani20
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Comment: C: Extracting sample ID and their genotypes
... No, my data format is not VCF. ...
written 20 months ago by Siavash Salek Ardestani20
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Comment: C: Extracting sample ID and their genotypes
... 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 Ardestani20
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Extracting sample ID and their genotypes
... 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 ...
next-gen chip-seq snp written 20 months ago by Siavash Salek Ardestani20 • updated 20 months ago by paolo002160
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Gene symbol list
... Hi, I have many coordinates (approximatly1000), I want to know how can I find the gene symbols that are in these coordinates? Thanks, Siavash ...
sequence next-gen chip-seq snp written 2.2 years ago by Siavash Salek Ardestani20 • updated 2.2 years ago by Alex Reynolds30k
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expected heterozygosity calculation
... 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 ...
vcf genome snp written 2.2 years ago by Siavash Salek Ardestani20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... Hi Thank you for useful comment. Yes of course, I did it. The best, Siavash ...
written 2.3 years ago by Siavash Salek Ardestani20

Latest awards to Siavash Salek Ardestani

Popular Question 9 months ago, created a question with more than 1,000 views. For Number of threads in BWA
Popular Question 16 months ago, created a question with more than 1,000 views. For SNP,INDEL counting per chromosomes in vcf
Popular Question 19 months ago, created a question with more than 1,000 views. For SNP,INDEL counting per chromosomes in vcf

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