User: amitgourav.ghosh12

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Posts by amitgourav.ghosh12

<prev • 29 results • page 1 of 3 • next >
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Comment: C: Change rsID to chromosome:location in bim files for plink
... Thank you very much again! I could do it. ...
written 9 days ago by amitgourav.ghosh1240
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Comment: C: Change rsID to chromosome:location in bim files for plink
... Thank you very much! I shall try out at once. ...
written 10 days ago by amitgourav.ghosh1240
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Change rsID to chromosome:location in bim files for plink
... Some of the SNPs in my dataset are without rs ids, so in the bim file, they have dots instead of rs ids for them. So for errorless analysis how should replace the rs id column with that of the chromosome: location column instead? ...
genome plink snp written 10 days ago by amitgourav.ghosh1240 • updated 9 days ago by chrchang5235.0k
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Comment: C: VCFtools: --window-pi and --from-bp --to-bp produces different start and ending
... Hello Sir, I am facing the same problem. I somewhat managed to get one whole region to come as one in Tajima's D calculation but I am unable to do so for the pi calculation. Did you find a way to overcome this problem? I yes, can you please suggest me what to do? Thanking you, Amit ...
written 12 months ago by amitgourav.ghosh1240
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Comment: C: Tajima's D Using SNP data ONLY
... Even I also have SNP data, can you please suggest how to compute Tajima's D without vcf files? Thank you! ...
written 13 months ago by amitgourav.ghosh1240
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Comment: C: How to do Tajima's D analysis?
... Hello Sir, indeed there are plenty of questions in the site. What I learnt till now is that one can use the package "pegas" in R or use dnasp v.5 or vcf tools for this purpose. I have binary format files from plink and the individuals respective MAFs, but not sequences. I am planning to download vcf ...
written 13 months ago by amitgourav.ghosh1240
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How to do Tajima's D analysis?
... Can anyone please suggest how to do Tajima's D analysis and the software required? Or can you please provide me with the links of similar answers. I want to detect signature of positive selection of certain alleles in my database. ...
genome snp written 13 months ago by amitgourav.ghosh1240
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... Yes I plan to do so, I tried plotting it in R using ggplot, the colour reference took up the whole area instead of the plot. I managed to plot it in Excel with the colours, but I presume it is mostly for visualisation only. The name of the add-in is XLMiner Data Visualisation. If I point the cursor ...
written 14 months ago by amitgourav.ghosh1240
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... I just finished counting the unique population groups in the samples. There were 254 different ethnicities in the sample size of 1977. ...
written 14 months ago by amitgourav.ghosh1240
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Comment: C: How to do pca plot from .eigenval and .eigenvec files from Plink in R.
... Great! I feel this is exactly what I wanted. Thank you Sir! Regarding Abkhazia, yes you are almost correct. This region is bit norther up in Georgia. Situated in the eastern coast of Black Sea. Last but not the least, it is a disputed territory of Georgia which enjoyed some autonomy while it was pa ...
written 14 months ago by amitgourav.ghosh1240

Latest awards to amitgourav.ghosh12

Supporter 9 days ago, voted at least 25 times.
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Removing SNPs with over 2% missing rate in plink
Popular Question 11 months ago, created a question with more than 1,000 views. For How to do pca plot from .eigenval and .eigenvec files from Plink in R.

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