User: Ana

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Ana100
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Posts by Ana

<prev • 92 results • page 1 of 10 • next >
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SNPs in high LD after LD pruning
... Hello all, I have question, sorry in advance if it is so simple but I am just slightly puzzled. I am trying to use LD pruned set of SNPs for my population genomics analysis. I am using SNPrelate and directly parse the vcf file into the package. For the species that I am working with, LD decays quit ...
ld snprelate written 12 days ago by Ana100 • updated 12 days ago by Kevin Blighe28k
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Comment: C: VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
... No, I did not get any error message. I just get only 1 million SNPs in the table and I do not know which of them from the main vcf file ...
written 7 weeks ago by Ana100
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VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
... I am trying to convert my vcf file to a flat tab-separated format by using "VariantsToTable" in GATK. I am particularly interested in DP at the sample annotation for my analysis. I am using /data/programs/gatk-4.0.4.0/gatk VariantsToTable -V final.vcf -GF DP -O snps.DP.tab My vcf file cons ...
gatk written 7 weeks ago by Ana100 • updated 7 weeks ago by finswimmer5.4k
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tools to align DNA sequences against protein sequence
... Hi all, I need to map a bunch of fastq files consisting of DNA sequences (paired end reads) against pan-genome proteins. So I need to align DNA sequences against proteins sequences. I used DIAMOND (which was very fast and user friendy), however later on I figured out it does not support paired-end ...
dna sequence alignment fastq files written 8 weeks ago by Ana100
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hypergeometric test on outlier SNPs
... Hi all, I have done some genome scan analyese with 2 different methods to identify outlier SNPs. There are some overlapping between these 2 methods. I want to know if the observed overlap between these 2 methods is any better than that obtained by chance alone? I have read different pots(https://sta ...
outliers hypergeometric test R written 10 weeks ago by Ana100
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TukeyHSD does not match the box plot
... Hi all, I have done anova followed by Tukey for multiple comparisons to compare the depth of coverage between different genotypes (homozygote for reference allele, homozygote for alternative allele and heterozygote) on different chromosomes. The strange thing is that, Tukey shows sifinificat differ ...
anova depth of coverage written 10 weeks ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Yes, I see you point. When to increase the dimension to 4 you will not get the error. But first, please note that the solution that Nicolas suggested computes correlation between the mean of DP for hom and het. So, it end up having 2 values and cor.test does not work for it. Second, the length of ho ...
written 4 months ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... No, I do not think so. I get this error from running cor.test and I run the cor.test between homozygotes.mean.common$dp (=7.61) and heterozygotes.mean.common$dp (=6.5). So only 2 values. I am not sure of this is the best approach to proceed! I am trying to find if there is any way to compute correl ...
written 4 months ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Not quite sure if I get your point. The error says I need to have at least 3 non-NA values for the correlation test. `cor.test(homozygotes.mean.common$dp,heterozygotes.mean.common$dp)` this computes correlation between only 2 values, which I guess is the reason of error. ...
written 4 months ago by Ana100
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Comment: C: compute correlation for depth of coverage between 2 datasets with different leng
... Yes, already found this. But, my data-set does not have any NA. I am not quite how this going to work. By calculating the mean I get one mean value for 0|0 genotype and one vale for heterozygote genotype. So, I will have only 2 values for the co.test! ...
written 4 months ago by Ana100

Latest awards to Ana

Popular Question 4 weeks ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 5 weeks ago, created a question with more than 1,000 views. For how to filter vcf file based on sample DP? vcf tools does not work
Popular Question 4 months ago, created a question with more than 1,000 views. For how to filter vcf file based on sample DP? vcf tools does not work
Supporter 8 months ago, voted at least 25 times.

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