User: rthapa

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rthapa10
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7 hours ago
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2 years, 8 months ago
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r*****@tamu.edu

Posts by rthapa

<prev • 60 results • page 1 of 6 • next >
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Copy number variation data for population structure analysis
... Hi, Does anyone have any idea if there is any tool available to detect population structure from copy number data rather than SNP data? Thanks ...
cnv written 3 days ago by rthapa10 • updated 2 days ago by khalid.belkhir30
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Comment: C: B allele frequency (BAF)
... Thanks a lot but the genome I am using is not the human genome. ...
written 9 days ago by rthapa10
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Comment: C: B allele frequency (BAF)
... Not from Illumina genotyping array but from vcf file generated from NGS data. ...
written 9 days ago by rthapa10
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B allele frequency (BAF)
... Hi, I want to calculate B allele frequency from a vcf file. I found that vcftools can be used to estimate allele frequency of REF allele and ALT allele. I wonder if vcftools could also estimate B allele frequency. Are there other tools that we could use for calculation BAF from vcf file? Thanks ...
snp written 9 days ago by rthapa10 • updated 8 days ago by bernatgel2.6k
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Issue on downloading fastPHASE in Mac
... Hi, I am trying to download fastPHASE in mac. I have downloaded macOSfp.tar. It looks like there should be 5 files inside the folder after unzipping but I only have one. Does anyone have any idea? Thanks ...
fastphase written 5 weeks ago by rthapa10
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Comment: C: KaryoploteR for copy number
... Thank you for the advice. Here is the example of a plot I want to make. I didn't find a way to insert the image here. https://media.springernature.com/full/springer-static/image/art%3A10.1186%2Fs12864-015-2096-x/MediaObjects/12864_2015_2096_Fig4_HTML.gif The input file looks like, CHROM ST ...
written 3 months ago by rthapa10
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KaryoploteR for copy number
... Hi, I am trying to plot a genome-wide Copy number variation using KaryoploteR. I am getting an error saying duplicate chromosome names in the genome. But I have CN in several locations of the same chromosome. Does anyone have any idea? Thanks > head(custom.genome) GRanges object with 6 ...
genome karyoploter written 3 months ago by rthapa10 • updated 3 months ago by Philipp Bayer6.7k
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quality check of vcf files
... Hi, I have a multiple vcf files for the same sample. I want to select the best single vcf file from all. I don't know the sequencing depth of the samples. I wonder if there is a way to select the best one based on the quality scores of SNP calls from the vcf files. Thanks ...
vcf snp written 3 months ago by rthapa10 • updated 3 months ago by a.alnawfal.199240
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CNVRs visualization with karyoploteR
... Hi, I am using karyoploteR to visualize CNV. I am getting following error. But I do have the genomic region in a bed file. Could anyone provide a suggestion what might have gone wrong? Error in plotKaryotype(zoom = "Chr01:3647-12170735", main = "BedGraphs", : You are trying to set the zoom to ...
cnv written 4 months ago by rthapa10
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Phenotypic evaluation of significant SNPs from GWAS result
... It might be a basic question but I am having difficulty on finding the significant differences of phenotypes for a significant SNP. The phenotypic data I have is in the ordinal scale (1,2,3,4,5). I have done GWAS analysis found some significant SNPs. I am trying to see if the SNP is not false positi ...
snp written 5 months ago by rthapa10

Latest awards to rthapa

Popular Question 10 months ago, created a question with more than 1,000 views. For best value of lfc threshold
Popular Question 16 months ago, created a question with more than 1,000 views. For transcript count after string tie merge

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