User: rthapa
rthapa • 10
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- 2 years, 8 months ago
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Posts by rthapa
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... 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 ...
written 3 days ago by
rthapa • 10
• updated
2 days ago by
khalid.belkhir • 30
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2
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95
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2
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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
rthapa • 10
0
votes
2
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95
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2
answers
Comment:
C: B allele frequency (BAF)
... Not from Illumina genotyping array but from vcf file generated from NGS data. ...
written 9 days ago by
rthapa • 10
0
votes
2
answers
95
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2
answers
... 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
...
0
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82
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... 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 ...
written 5 weeks ago by
rthapa • 10
0
votes
1
answer
202
views
1
answers
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
rthapa • 10
0
votes
1
answer
202
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1
answer
... 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 ...
written 3 months ago by
rthapa • 10
• updated
3 months ago by
Philipp Bayer ♦ 6.7k
1
vote
1
answer
161
views
1
answer
... 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 ...
written 3 months ago by
rthapa • 10
• updated
3 months ago by
a.alnawfal.1992 • 40
0
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0
answers
119
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... 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 ...
written 4 months ago by
rthapa • 10
0
votes
0
answers
121
views
0
answers
... 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 ...
written 5 months ago by
rthapa • 10
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Popular Question
10 months ago,
created a question with more than 1,000 views.
For best value of lfc threshold
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16 months ago,
created a question with more than 1,000 views.
For transcript count after string tie merge
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