User: Ana

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Ana170
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Posts by Ana

<prev • 97 results • page 1 of 10 • next >
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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 11 weeks 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 3 months ago by Ana170 • updated 3 months ago by Alex Reynolds28k
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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 4 months ago by Ana170 • updated 4 months ago by benformatics920
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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 5 months ago by Ana170 • updated 5 months ago by Alex Reynolds28k
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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 8 months ago by Ana170 • updated 8 months ago by Fabio Marroni2.3k
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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 10 months ago by Ana170 • updated 10 months ago by Kevin Blighe45k
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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 11 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 11 months ago by Ana170 • updated 10 weeks 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 11 months ago by Ana170
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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 12 months ago by Ana170

Latest awards to Ana

Popular Question 3 months ago, created a question with more than 1,000 views. For determining appropriate window size for identifying highly differentiated SNPs
Centurion 3 months ago, created 100 posts.
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 run STRUCTURE command n times for each K value?
Popular Question 5 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 6 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 8 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 10 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 10 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 10 months ago, created a question with more than 1,000 views. For 012 genotype matrix using vcf tools (converting rows to columns)
Popular Question 10 months ago, created a question with more than 1,000 views. For extract sample DP values from VCF
Popular Question 11 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 14 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
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