User: bwczech

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bwczech70
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Posts by bwczech

<prev • 72 results • page 1 of 8 • next >
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Ok, thank you! Now I understand, but which value should I use for lambda in Poisson distribution. I would like to test this using Kolmogorov-Smirnov. I have vector with number of SNPs in each 100kb non-overlapping windows, but for testing whether the numer of SNPs is random (random number of SNPs = ...
written 5 weeks ago by bwczech70
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Ok. Thank you. I still do not understand, why I can't use a uniform distribution to check whether the number of variants in windows (non-overlapping) is randomly distributed or is constant ...
written 6 weeks ago by bwczech70
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Checking regions with high density of SNPs
... Hi, I calculated number of SNPs in non-overlapping windows in each chromosome. I found regions with extreme numbers of SNPs in compare to other windows. How can I check this region/window? What software can I use to check if this region contain many genes or sth else? I would like do it based on GF ...
snps high density written 6 weeks ago by bwczech70
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Thank you. Could you tell me where can I find information that to test inter-SNP distance I should use gamma distribution and Poisson distribution for number of snps in windows? I need a reference why I am using this distribution instead of uniform distribution. ...
written 6 weeks ago by bwczech70
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Thank You! I have another question. I have also information about distance of the snp to the cloest indel. Should I also use a gamma distribution to check whether snps are close to indels or if it is a randomness? And the same question about length of indels. To check whether long of indels (Bp) i ...
written 6 weeks ago by bwczech70
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Test of probability of length of variation of indels
... Hi, I have file with InDels length (in bp). Could tell me how can I check whether the variation of InDels length occurs with the same probability (randomness)? I think I should use Kolmogorov Smirnov, but I have no idea which probability should I use or any other function in R. Thank you for your ...
randomness indels test written 6 weeks ago by bwczech70
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Comment: C: Testing uniform distribution of SNPs across chromosome
... Ok, thank you guys. So should I test whether inter-SNP distances (between two closest SNPs) have Poisson or Gamma distribution? Which distribution should I use? Poisson is discrete distribution, and Gamma is continuous. and what about other information that can I used: e.g. I can divide chromosome ...
written 6 weeks ago by bwczech70
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Comment: C: VCF - InDels and SNPs relation
... wow! Thank you, I did not know this site of bedtools. How can I understand zeros? That''s mean that SNP is inside indel? ...
written 6 weeks ago by bwczech70
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Comment: C: Testing uniform distribution of SNPs across chromosome
... I mean uniform distributed within a chromosome. I have files with distance between SNPs to the closest, but I have no idea how to check uniform distribution based on this. ...
written 6 weeks ago by bwczech70
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Testing uniform distribution of SNPs across chromosome
... Hi, Could you tell me, how can I test, whether distribution of SNPs across each chromosome is uniform? Any soft, or idea how can I test it? ...
vcf uniform snp written 6 weeks ago by bwczech70

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Popular Question 5 weeks ago, created a question with more than 1,000 views. For Number of SNPs in VCF
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Number of SNPs in VCF
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Popular Question 11 months ago, created a question with more than 1,000 views. For Cluster analysis for SNPs data in R
Popular Question 11 months ago, created a question with more than 1,000 views. For Comparing two columns and replace in R Package

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