User: siyavash_damdar
siyavash_damdar • 20
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Posts by siyavash_damdar
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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 3 months ago by
siyavash_damdar • 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 10 months ago by
siyavash_damdar • 20
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... No, my data format is not VCF. ...
written 10 months ago by
siyavash_damdar • 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 10 months ago by
siyavash_damdar • 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 10 months ago by
siyavash_damdar • 20
• updated
10 months ago by
paolo002 • 150
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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 15 months ago by
siyavash_damdar • 20
• updated
15 months ago by
Alex Reynolds ♦ 28k
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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 16 months ago by
siyavash_damdar • 20
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... Hi
Thank you for useful comment. Yes of course, I did it.
The best,
Siavash ...
written 16 months ago by
siyavash_damdar • 20
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... sorry if bother you. Thanks ...
written 17 months ago by
siyavash_damdar • 20
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602
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... so, according to your comments, I can have 3 scenarios:
1. call sample by sample and joint genotype
2.call all samples per region
3. call all samples (all regions) using multithreading
so, Are there any differences in the results (genotypes) of these scenarios?
...
written 17 months ago by
siyavash_damdar • 20
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