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User: siyavash_damdar

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Posts by siyavash_damdar

<prev • 39 results • page 1 of 4 • next >
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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 8 weeks ago by siyavash_damdar • 20
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Comment: C: Extracting sample ID and their genotypes
... No, my data format is not VCF. ...
written 8 weeks ago by siyavash_damdar • 20
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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 8 weeks ago by siyavash_damdar • 20
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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 8 weeks ago by siyavash_damdar • 20 • updated 8 weeks ago by paolo002 • 100
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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 7 months ago by siyavash_damdar • 20 • updated 7 months ago by Alex Reynolds ♦ 27k
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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 8 months ago by siyavash_damdar • 20
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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 8 months ago by siyavash_damdar • 20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... sorry if bother you. Thanks ...
written 9 months ago by siyavash_damdar • 20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... 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 9 months ago by siyavash_damdar • 20
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Comment: C: variant calling for more than 60 samples using haplotype caller
... what are you thinking if I increase my memory an thread (RAM 64 and 16 thread)? ...
written 9 months ago by siyavash_damdar • 20

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