User: oselm

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oselm30
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Posts by oselm

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Comment: C: Bcftools homozygous calls have less read counts than heterozygotes
... It's not easy to generalize as there are 150 individuals x 10 M SNPs. Anyway, here I show three examples of SNPs predominantly homozygous-consensus, heterozygous and homozygous-alternative. Homozygous-consensus: CHR1 2725 . C T 225.009 PASS MQSB=0.924584;MQ0F=0;AF1=0;AC1=0;MQ=60;FQ=-53.986 ...
written 6 weeks ago by oselm30
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Bcftools homozygous calls have less read counts than heterozygotes
... Dear all, I am trying to call SNPS across 150 individuals of a non-model species genotyped using a WGS resequencing approach. In short: I aligned reads from each sample against the reference using BWA and subsequently used bcftools mpileup to calculate the counts and bcftools call to call genotyp ...
vcf population genomics bcftools filtering bwa written 7 weeks ago by oselm30
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Comment: C: Anomal pvalue distribution and qvalue calculation
... Pi0est returns: $pi0 [1] 0.5676673 $pi0.lambda [1] 0.9271837 0.8510835 0.7918458 0.7430548 0.7095104 0.6840553 0.6615802 0.6438723 0.6268776 [10] 0.6143542 0.6053025 0.5967893 0.5902369 0.5834115 0.5833420 0.5778953 0.5764620 0.5848014 [19] 0.5900136 $lambda ...
written 8 months ago by oselm30
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Anomal pvalue distribution and qvalue calculation
... I am working on differential gene expression data ans I am using the qvalue R package to calculate qvalues of out of this pvalues distribution: ![Pval distribution][1] The lowest qs are around 0.22. If we have a look at the p-values histogram, we see that there are actually more low ps than expe ...
rna-seq q-value written 8 months ago by oselm30
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R dendrogram by cluster
... Hi all, I am using R to plot a dendrogram of a hierarchial clustering. I have realised a hierarchical clustering of ~3000 elements. The plot of the corresponding tree is obviously super messy. These 3000 elements are clustered in 20 groups using the cutree function. What I want is to plot the tr ...
R dendrogram written 23 months ago by oselm30 • updated 15 months ago by Biostar ♦♦ 20
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PCA of a genotype matrix
... Hi all, I have a question concerning the methods to perform a Principal Component Analysis of genotype matrix (genotypes coded as 0,1,2) to study the structure of a population. I have been exposed to two different ways of performing this analsys, and I don't understand the differences between th ...
pca snp written 2.2 years ago by oselm30 • updated 2.2 years ago by anp375140
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batch effect in radseq
... Hi all, We sent 600 samples of a plant species (no reference genome) for DNA-extraction, library prep and ddRadSeq (paired end, Illumina Hiseq). Firstly, 200 samples were sequenced as pilot, then the others 400 followed the same procedure. The raw reads were then: - Demultiplexed and adepter clip ...
radseq snp batch effect written 2.3 years ago by oselm30 • updated 2.1 years ago by Biostar ♦♦ 20

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Popular Question 23 months ago, created a question with more than 1,000 views. For PCA of a genotype matrix

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