User: Abdul Rafay Khan

gravatar for Abdul Rafay Khan
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Karachi, PK
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5 years, 5 months ago
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Contact: alrafaykhan@gmail.com

Posts by Abdul Rafay Khan

<prev • 83 results • page 1 of 9 • next >
2
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177
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Add sample number/name column to VEP result
... Is there any way to add a sample number/name column to VEP result file when the merge vcf file of multiple samples is annotated with VEP. ...
vcf vep written 5 months ago by Abdul Rafay Khan1.1k • updated 5 months ago by Emily_Ensembl20k
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208
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Multi samples VCF file manipulation
... I have VCF file with multiple samples. How to list down the SNP present in more than one sample with sample ids. ...
vcf written 6 months ago by Abdul Rafay Khan1.1k
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223
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Comment: C: LOD Score NaN Error
... but my data seems correct ...
written 10 months ago by Abdul Rafay Khan1.1k
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249
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How to perform fst test using SNPs frequency?
... How to perform fst test using SNPs frequency? My data format: SNPs Pop1 Pop2 Pop3 Pop4 Pop4 Pop5 Pop6 Pop7 rs2740574 0.974 0.9448 0.7921 0.9625 0.9616 0.902 0.3556 0.9161 rs1751034 0.8906 0.7586 0.798 0.8457 0.8223 0.8081 0.7413 0.747 ...
fst snp written 10 months ago by Abdul Rafay Khan1.1k
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LOD Score NaN Error
... library(paramlink) y = read.table("markers.txt", header=TRUE) x = linkdat(y, model=1) lod(x) Result: LOD: NaN **Data:** FAMID ID FID MID SEX AFF M_A1 M_A2 1 1 0 0 1 1 2 3 1 2 0 0 2 1 1 2 1 3 1 2 2 2 2 2 1 4 1 2 1 2 2 3 1 5 1 2 2 1 1 2 1 ...
lod score paramlink R written 10 months ago by Abdul Rafay Khan1.1k • updated 10 months ago by zx87549.1k
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(Closed) How to perform fst test using SNPs frequency?
... How to perform fst test using SNPs frequency? My data format: SNPs Pop1 Pop2 Pop3 Pop4 Pop4 Pop5 Pop6 Pop7 rs2740574 0.974 0.9448 0.7921 0.9625 0.9616 0.902 0.3556 0.9161 rs1751034 0.8906 0.7586 0.798 0.8457 0.8223 0.8081 0.7413 0.747 rs1414334 0.875 0.8453 0.7872 0.8831 0. ...
frequency fst snp written 10 months ago by Abdul Rafay Khan1.1k
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Comment: C: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
... Hey Kelvin, How to plot sub-population ("ACB","ASW","ESN","GWD","LWK","MSL","YRI", "CLM","MXL","PEL","PUR", "CDX","CHB","CHS","JPT","KHV", "CEU","FIN","GBR","IBS","TSI", "BEB","GIH","ITU","PJL","STU") in pca plot instead of "African","Hispanic","East-Asian","Caucasian","South Asian"? ...
written 10 months ago by Abdul Rafay Khan1.1k
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How to convert population SNPs frequency data into Plink format?
... How to convert population SNPs frequency data into Plink format? My format: > SNP Ashkenazi Finnish European Other African/African American Latino East Asian > rs2234922 0.1448 0.1567 0.1995 0.1965 0.3388 0.1076 0.1253 > rs3812718 0.5035 0.5446 ...
plink snp written 10 months ago by Abdul Rafay Khan1.1k
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(Closed) Minor allele frequency and fst test
... I have SNPs data in the form of minor allele frequency of different populations, how to calculate the fst test using this data and can we load such data in plink 1.9? My data format: SNP Ashkenazi Jewish_G Finnish_G Non-Finnish European_G Other_G African/African American_G Latino_G East Asian ...
maf fst written 10 months ago by Abdul Rafay Khan1.1k
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How do I calculate the haplotype frequencies in 1000 genome populations
... > I have haplotypes (CYP2D6.1, CYP2D6.2, CYP2D6.3, CYP2D6.4, CYP2D6.5, > CYP2D6.6) How do I calculate the haplotype frequencies these haplotypes in 1000 genome populations? ...
populations haplotype 1000 genome frequencies written 11 months ago by Abdul Rafay Khan1.1k

Latest awards to Abdul Rafay Khan

Great Question 5 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Librarian 5 months ago, created a post with more than 10 bookmarks. For Tools to merge overlapping paired-end reads
Popular Question 5 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 5 months ago, created a question with more than 1,000 views. For Why not Windows
Appreciated 10 months ago, created a post with more than 5 votes. For Tools to merge overlapping paired-end reads
Popular Question 10 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Prophet 10 months ago, created a post with more than 20 followers. For Tools to merge overlapping paired-end reads
Guru 10 months ago, received more than 100 upvotes.
Popular Question 12 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 14 months ago, created a question with more than 1,000 views. For Run BLAST on Linux terminal
Popular Question 14 months ago, created a question with more than 1,000 views. For Why not Windows
Student 14 months ago, asked a question with at least 3 up-votes. For Why not Windows
Great Question 22 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal
Epic Question 22 months ago, created a question with more than 10,000 views. For Install and Run R on Linux
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Popular Question 22 months ago, created a question with more than 1,000 views. For Best Variation Analysis Software which can support VCF file Format?
Popular Question 22 months ago, created a question with more than 1,000 views. For Unix or Linux which is better choice for genomic analysis?
Popular Question 22 months ago, created a question with more than 1,000 views. For Bowtie2 vs Tophat Whats the difference
Student 22 months ago, asked a question with at least 3 up-votes. For Why not Windows
Scholar 22 months ago, created an answer that has been accepted. For A: MaSuRCA Assembler runCA Error
Supporter 22 months ago, voted at least 25 times.
Great Question 23 months ago, created a question with more than 5,000 views. For Run BLAST on Linux terminal

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