User: akang

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akang90
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Posts by akang

<prev • 67 results • page 1 of 7 • next >
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Local blast with multiple databases and multiple files
... I am trying to run a specific query against specific custom database in python. When i just use one database it works fine but doesnt produce any result (just empty output file) when run my queries against multiple databases. Any suggestions? db1=os.path.join(path, "ref/db1.fasta") db2=os.p ...
python blast written 5 weeks ago by akang90
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Extracting amino acid positions from a fasta sequence
... I need a suggestion regarding extracting positions from a nucleotide fasta file. I have a fasta file like below. I am aligning the file ,then converting the sequences into amino acid sequence and finally extracting specific amino acids (say position 1,3,4) from the amino acid data. But since their ...
fasta python written 6 weeks ago by akang90 • updated 6 weeks ago by rpolicastro3.9k
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Comment: C: R, plot text table
... Since it is a biological dataset I think Biostars community suits it the best. This particular problem aims at visualizing a viral gene segment from different samples and understand its origin. There are all sort of biological datasets and this might be a new one for the community. Here is an examp ...
written 20 months ago by akang90
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Comment: C: R, plot text table
... Added some information about the example data. ...
written 20 months ago by akang90
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Should the values of pairwise genetic distances and Fst be somewhat similar?
... I have used an R package called Adegenet to calculate pairwise Fst and pairwise genetic distances from an alignment file. But both the values are completely different. matFst <- pairwise.fst(mydata,res.type="matrix") #pairwise Fst temp <- pairDistPlot(mydata, other(mydata)$pop) # pai ...
R adegenet written 2.3 years ago by akang90
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Change the font size of the Y axis of a boxplot
... I have calculated the pairwise distances between populations using adegenet (R package) and have plotted them using a boxplot. Labels on the Y axis are overlapping so i want to change the font size. How do I do that? Here is my code temp <- pairDistPlot(mydata, grp=mydata$pop) temp$boxpl ...
boxplot R adegenet written 2.3 years ago by akang90
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Within and between mean group genetic distance greater than 1 with MEGA X
... I have 5 groups in my study and I found that within and between mean group genetic distance is greater than 1 when calculated with MEGA X. Can someone help me understand what does that mean? ...
genetic distance written 2.3 years ago by akang90
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Calculate effective population size (Ne)
... Is there a program that can calculate effective population size (Ne) based on haploid sequence data? Most programs work with diploid SNP data as I know. ...
effective population size sequence data ne written 2.4 years ago by akang90 • updated 6 weeks ago by chenyangkang240
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Answer: A: Estimating heritability using GCTA or LDAK in an admixed population
... You can use kinship matrix or GRM which accounts for population structure. For LDAK see –calc-kins-direct and for GCTA see --grm. ...
written 3.5 years ago by akang90
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Comment: C: How to calculate Imputation Accuracy Estimates like concordance with BEAGLE?
... I'm trying to do the same thing..just that my data is multi allelic. How do we calculate imputation accuracy for multi allelic data? Ill appreciate any help on that.Thanks! ...
written 3.7 years ago by akang90

Latest awards to akang

Great Question 20 months ago, created a question with more than 5,000 views. For How to plot LD decay?
Popular Question 20 months ago, created a question with more than 1,000 views. For Request for BEAGLE tutorial
Popular Question 20 months ago, created a question with more than 1,000 views. For Convert beagle output file to plink
Popular Question 20 months ago, created a question with more than 1,000 views. For Deleting the Individuals from genlight/genind object in adegenet
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Deleting the Individuals from genlight/genind object in adegenet
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Phylogenetic tree in Adegenet
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Phylogenetic tree in Adegenet
Popular Question 2.4 years ago, created a question with more than 1,000 views. For How to increase the resolution of the figures for publication
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to increase the resolution of the figures for publication
Popular Question 3.5 years ago, created a question with more than 1,000 views. For CNV calling and analysis from Affymetrix Axiom 50K SNP chip
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to plot LD decay?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Request for BEAGLE tutorial
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Converting 0 1 2 in a format recognized by plink
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Genotype count in a VCF file
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How to determine the haplotypes using Beagle
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Population-wise decay of linkage disequilibrium (LD)

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