User: Ana

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Ana130
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Posts by Ana

<prev • 94 results • page 1 of 10 • next >
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How to add significance level to correlation heatmap using ggplot2
... I have generated some correlation heatmaps. I want to know how can I replace r-values in each cell of the plot with the p-value? These value inside the heatmap are correlation coefficients, I want to replace them with the p-values, or have both p-value and r-value in each cell! This is my R-table ...
R ggplot correlation written 11 days ago by Ana130 • updated 11 days ago by Alex Reynolds27k
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genomic inflation factor and how to use it to estimate adjusted P-values in GWAS?
... Hi all, I have 3 questions regarding genomic inflation factor and how to use it to estimate adjusted p-value. I would appreciate any help. I am running genotype environment association analysis by using latent factor mixed model (LFMM). I am using this to estimate genomic inflation factor: lam ...
lambda gwas written 3 months ago by Ana130 • updated 3 months ago by Fabio Marroni2.1k
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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 5 months ago by Ana130 • updated 5 months ago by Kevin Blighe37k
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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 6 months ago by Ana130
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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 6 months ago by Ana130 • updated 6 months ago by finswimmer10.0k
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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 6 months ago by Ana130
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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 7 months ago by Ana130
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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 7 months ago by Ana130
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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 9 months ago by Ana130
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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 9 months ago by Ana130

Latest awards to Ana

Popular Question 11 days ago, created a question with more than 1,000 views. For difference between read depth (DP) at site (INFO) and sample(FORMAT) level
Popular Question 5 weeks ago, created a question with more than 1,000 views. For difference between read depth (DP) at site (INFO) and sample(FORMAT) level
Popular Question 3 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 5 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 5 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
Popular Question 5 months ago, created a question with more than 1,000 views. For 012 genotype matrix using vcf tools (converting rows to columns)
Popular Question 5 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 6 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
Popular Question 9 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 13 months ago, voted at least 25 times.

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