User: Ana

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Ana170
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Posts by Ana

<prev • 98 results • page 1 of 10 • next >
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haplotype network analysis with Pegas package in R
... Hi all, I am very new in haplotype analysis and have faced with some problems that I do not know how to solve. I want to generate haplotype networks for sodium channel (DKr gene) in anopheles species. I have converted my vcf into fast file, produced multiple alignment with ClustalW and I am using "P ...
R pegas haplotype written 4 weeks ago by Ana170
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how to calculate genetic position for each marker from the genetic map file?
... Hello, I want to calculate genetic position for my SNPs (~ 1million) to make a map file. I have a genetic map file. head genetic_map chr pos LG cM Chr01 1 0.01 Chr01 1000001 0.48 Chr01 2000001 2.83 Chr01 3000001 5.26 How can I use the genetic map file to calculate genetic ...
map file genetic position written 13 months ago by Ana170
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how to assign SNPs to each gene with overlapping intervals in r?
... Hi all, I have ~900K SNPs and I want to assign them to genes based on their positions. here is a very simple example of what I am doing: the first data set contains SNPs and their positions on each chromosome (here I am showing only chromosome 1, but I have 17 chromosomes in total) data.s ...
R written 14 months ago by Ana170 • updated 14 months ago by Alex Reynolds30k
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Assign a genomic region to a window
... I am dealing with a bunch of inversions and running some analysis on each of them .One of them is located on chrommose one, the starting position is 6199548 and ending position is 9699260. So the length of this position is 3499712 bp. I want to generate non-overlapping windows based on the length o ...
R bioconductor windows genomicranges written 14 months ago by Ana170 • updated 14 months ago by benformatics1.6k
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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 15 months ago by Ana170 • updated 15 months ago by Alex Reynolds30k
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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 18 months ago by Ana170 • updated 18 months ago by Fabio Marroni2.5k
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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 20 months ago by Ana170 • updated 20 months ago by Kevin Blighe59k
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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 22 months ago by Ana170
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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 22 months ago by Ana170 • updated 13 months ago by snehakoneru0
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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 22 months ago by Ana170

Latest awards to Ana

Popular Question 13 months ago, created a question with more than 1,000 views. For calculating genotype quality from genotype likelihood
Popular Question 13 months ago, created a question with more than 1,000 views. For convert population allele count data into population allele frequency
Popular Question 13 months ago, created a question with more than 1,000 views. For how to extract a random set of SNP from a SNP table
Popular Question 13 months ago, created a question with more than 1,000 views. For determining appropriate window size for identifying highly differentiated SNPs
Popular Question 13 months ago, created a question with more than 1,000 views. For how to adjust a Manhattan plot for bayes factor
Popular Question 13 months ago, created a question with more than 1,000 views. For error with running distruct.py in fastSTRUCTURE
Popular Question 13 months 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 13 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 13 months ago, created a question with more than 1,000 views. For how to run STRUCTURE command n times for each K value?
Popular Question 13 months ago, created a question with more than 1,000 views. For downloading bam files of phase 3 of 1000 genomes project
Popular Question 14 months ago, created a question with more than 1,000 views. For determining appropriate window size for identifying highly differentiated SNPs
Centurion 14 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 15 months ago, created a question with more than 1,000 views. For how to run STRUCTURE command n times for each K value?
Popular Question 15 months 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 16 months 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 18 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 20 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 20 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 20 months ago, created a question with more than 1,000 views. For 012 genotype matrix using vcf tools (converting rows to columns)
Popular Question 21 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 21 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 2.1 years 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
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